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stringlengths 0
46.9k
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|---|---|
Let us say my `_quarto.yml` has this snippet:
```yml
format:
pdf:
documentclass: book
include-in-header:
- tex/preamble.tex
- tex/macros.tex
include-before-body:
- tex/firstpages.tex
```
And inside `macros.tex` I have:
```latex
\newcommand{\mytitle}{{{< meta title >}}}
\newcommand{\myfullname}{{{< var author.fullname >}}}
\newcommand{\myshortname}{{{< var author.shortname >}}}
```
This won't work... Is there any way of replacing these shortcodes in the LaTeX files..? | {
"assignee": null,
"comments": 2,
"created_at": "2022-06-02T16:16:01Z",
"creator": "ramiromagno",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1047,
"state": "open",
"title": "Question: Is it possible to use shortcodes in LaTeX macros?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1047"
} |
## Problem I am experiencing
When a code block produces a plot, that plot is saved in a subdirectory in the same directory as the .qmd file.
The quarto project attempts to integrate easily with Hugo (for which I am forever grateful 🙂).
This location of the output doesn't work very nicely with Hugo though:
Hugo expects images to be in the `/static` directory, while the .qmd file lives in the `/content` directory.
The rendered .md file contains this line:
```md
```
But since the path is not the one expected by Hugo, the plot is not produced in the .html.
## Workaround
There is of course a workaround, but it is cumbersome and far from ideal:
1. Copy the figure (and the subdirectory structure) to `/static` (and remember to update the copy if the code changes: this hardcoding is far from great...)
3. Add anything in `/content/**/figure-gfm` directory to .gitignore because adding heavy files to `/content` makes the rendering of the website very slow and eventually breaks it (since Hugo will try to render anything that is in `/content`).
## Questions
So my questions are:
1. Did I miss something and am I doing things wrong?
2. If not, is there a way to have quarto save plots in `../../static/xxx/figure-gfm` instead of `xxx/figure-gfm` when the format is `hugo`?
Thank you!!!
## quarto check
[✓] Checking Quarto installation......OK
Version: 0.9.440
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.10.4
Path: /usr/bin/python3
Jupyter: 4.10.0
Kernels: julia-1.7, julia-1.5, julia-1.6, python3
[✓] Checking Jupyter engine render....OK
[✓] Checking R installation...........OK
Version: 4.2.0
Path: /usr/lib64/R
LibPaths:
- /home/marie/R/lib
- /usr/lib/R/library
rmarkdown: 2.14
[✓] Checking Knitr engine render......OK
## Checklist
When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you:
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, self-contained, and reproducible example?
- [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [x] upgraded to the latest version (including your versions of R, the RStudio IDE, and relevant R packages)?
| {
"assignee": null,
"comments": 4,
"created_at": "2022-06-02T00:53:21Z",
"creator": "prosoitos",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1044,
"state": "closed",
"title": "Location of plots not integrating well with Hugo",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1044"
} |
Thanks for the great work
I have uploaded the newest quarto version 498.
I used to be able to render my jupyter notebook with plotly plots in html
now I have the following message
Unable to display output for mime type(s): application/vnd.plotly.v1+json
How can I revert to previous versions of quarto?
All still works fine in qmd file but I would prefer to stick to Jupyter notebook
Thanks
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To file a _bug report_, please follow these instructions carefully: <https://yihui.org/issue/#bug-reports>
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## Checklist
When filing a _bug report_, please check the boxes below to confirm that you have provided us with the information we need. Have you:
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [x] included a minimal, self-contained, and reproducible example?
- [x] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [x] upgraded to the latest version (including your versions of R, the RStudio IDE, and relevant R packages)?
| {
"assignee": null,
"comments": 3,
"created_at": "2022-06-01T23:30:22Z",
"creator": "scalgary92",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1043,
"state": "closed",
"title": "Plotly plot not anymore rendered when using jupyter notebook in quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1043"
} |
Hello,
In rmarkdown html output, it was possible to allow a zoom on the included picture and the figure generated with the css and javascript described in the next link: [https://stackoverflow.com/questions/57313317/zoom-in-on-images-in-an-rmarkdown-rendered-to-flex-dashboard](https://stackoverflow.com/questions/57313317/zoom-in-on-images-in-an-rmarkdown-rendered-to-flex-dashboard)
I tested it in a quarto html website and it doesn't work. I don't really know css and javascript so I don't have any idea of how to adapt it.
Can I ask you if it would be possible for you to help me adapt it or even better to include something similar as a base functionnality of the html output?
I thank you in advance for your answer. | {
"assignee": null,
"comments": 2,
"created_at": "2022-06-01T05:01:41Z",
"creator": "Pierre9344",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1037,
"state": "closed",
"title": "Allow zoom on figure in quarto html output (more enhancement than issue)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1037"
} |
Using the `prompt/comment/collapse` options in an R chunk to simulate a CLI interaction does not seem to work. The `prompt` and `comment` options seem to be ignored. This file illustrates the issue:
````
---
execute:
echo: true
---
```{r, prompt = TRUE, comment = "", collapse = TRUE}
1 + 2
```
```{r}
#| collapse: true
#| prompt: true
#| comment: ""
1 + 2
```
````
| {
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"comments": 4,
"created_at": "2022-05-31T22:27:43Z",
"creator": "ltierney",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1035,
"state": "closed",
"title": "Using `prompt/comment/collapse` in an R chunk not working as in Rmarkdown",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1035"
} |
Reusing a chunk with `ref.label` seems to not be working when the chunk body is empty. It does work with a blank line for the body or when the body contains a `#|` option. This sample document illustrates the issue:
````
---
execute:
echo: true
---
The original chunk:
```{r}
#| label: foo
1 + 2
```
Using `ref.label` does not work with an empty body:
```{r, ref.label = "foo"}
```
Using `ref.label` does work with a blank line body:
```{r, ref.label = "foo"}
```
Using `<<...>>` noweb notation does work:
```{r}
<<foo>>
```
```` | {
"assignee": null,
"comments": 6,
"created_at": "2022-05-31T22:18:01Z",
"creator": "ltierney",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1034,
"state": "closed",
"title": "`ref.label` seems not to be handled quite right ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1034"
} |
This issue came up in the review of the accessible cheatsheets, see https://github.com/mine-cetinkaya-rundel/accessible-cheatsheets/issues/2#issuecomment-1095384374 for the original issue.
---
The following is a simplified version of the HTML output with `format: html` and `toc: true`:
```html
<!DOCTYPE html>
<html lang="en">
<head>
<title>Document Title</title>
</head>
<body>
<div id="quarto-content">
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
TABLE OF CONTENTS...
</div>
<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title">Document Title</h1>
</div>
</header>
DOCUMENT TEXT...
</main>
</div>
</body>
</html>
```
Three accessibility suggestions are:
1. Make `footer` available to HTML output via the yaml (like `page-footer` for websites, for example).
2. Move the table of contents into the `header`.
3. Move the `header` outside of `main`.
Similar to #1030, (2) and (3) might be things to address in Pandoc. I'm guessing (1) is addressable in Quarto.
| {
"assignee": null,
"comments": 0,
"created_at": "2022-05-31T20:21:04Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1032,
"state": "open",
"title": "Accessibility suggestions: Footers, table of contents, and headers",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1032"
} |
This issue came up in the review of the accessible cheatsheets, see https://github.com/mine-cetinkaya-rundel/accessible-cheatsheets/issues/4 for the original issue.
---
Suppose you have the following code chunk in a Quarto document with `format: html`.
```r
library(tidyverse)
mtcars %>%
filter(mpg > 30) %>%
ggplot(aes(x = mpg, y = disp)) +
geom_point()
```
The resulting HTML is as follows (with indentation added by me to make it a bit easier to read)
```html
<div class="sourceCode cell-code" id="cb5">
<pre class="sourceCode r code-with-copy">
<code class="sourceCode r">
<span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>mtcars <span class="sc">%>%</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">filter</span>(mpg <span class="sc">></span> <span class="dv">30</span>) <span class="sc">%>%</span></span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> mpg, <span class="at">y =</span> disp)) <span class="sc">+</span></span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_point</span>()</span>.
</code>
<button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button>
</pre>
</div>
```
Note that each line of code has an `href`. They're `area-hidden`, which is good, but the question is are they needed? Based on the original issue linked above:
- If the answer is "yes, they are needed", then "provide text within the links that describe the functionality and/or target of that link."
- If the answer is "no, they are not needed", then "remove the empty link".
cc @batpigandme | {
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"created_at": "2022-05-31T16:17:34Z",
"creator": "mine-cetinkaya-rundel",
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"labels": [
"accessibility"
],
"locked": false,
"milestone": "Future",
"number": 1030,
"state": "open",
"title": "Unused links in HTML output of code chunks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1030"
} |
```ERROR: Missing argument(s): command```
Expected according to ```quarto tools --help```: Show tool status
Tested with version 0.9.483. Has worked with version 0.9.407. | {
"assignee": null,
"comments": 0,
"created_at": "2022-05-31T14:24:55Z",
"creator": "TobiasHasenberg",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1028,
"state": "closed",
"title": "```quarto tools``` throws error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1028"
} |
## Use `scope = "col"` for all column headers denoted with `<th>` tags
This is, in effect, the same as the [gt issue #680](https://github.com/rstudio/gt/issues/680), opened by @jooyoungseo. This is currently missing from all of the tables I've generated based on the Quarto docs (e.g. markdown, `knitr::kable()`, DT, Python tabulate, etc.).
WCAG resources: [H63: Using the scope attribute to associate header cells and data cells in data tables](https://www.w3.org/TR/WCAG20-TECHS/H63)
## Use `<th scope="row">` for all row names
See @jooyoungseo's [gt issue #678](https://github.com/rstudio/gt/issues/678) for accessibility implications. In addition to gt, this applies to the default output for `knitr::kable()` and `DT::datatable()`, which include row names. Note also that the empty cell above the row names should be an empty `<td></td>` (as opposed to empty `<th></th>`, as it is now).
Let me know if you think it would be better to open this issue directly in knitr and DT.
WCAG resources: See H63 (above), and W3C WAI's [Tables with Two Headers](https://www.w3.org/WAI/tutorials/tables/two-headers/).
## Support multi-level and/or irregular headers?
I think this is currently out of scope for Quarto itself, as (thus far) I've only been able to generate such tables by using gt, kableExtra, and DT with a custom table container.
The easier of the two would be [Tables with Irregular Headers](https://www.w3.org/WAI/tutorials/tables/irregular/), which uses arguments to `<th>` (e.g. `<th colspan="2" scope="colgroup">` for two columns, or `<th rowspan="2" scope="rowgroup">` for two rows).
For [Tables with Multi-Level Headers](https://www.w3.org/WAI/tutorials/tables/multi-level/), such as those generated in gt and with kabelExtra, headers get `id`s, and are then associated with lower `<th>`, and `<td>` elements using `headers="foo bar baz"`.
Watch related [issue #926 for gt](https://github.com/rstudio/gt/issues/926) for @rich-iannone's forthcoming implementation. | {
"assignee": null,
"comments": 3,
"created_at": "2022-05-31T10:35:29Z",
"creator": "batpigandme",
"is_pull_request": false,
"labels": [
"accessibility"
],
"locked": false,
"milestone": "Future",
"number": 1025,
"state": "open",
"title": "Improve table markup for accessibility (a11y issue)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1025"
} |
I just noticed how the latest build(s) of quarto renders mermaid diagrams as png images instead of the natively supported ` ``` mermaid ` blocks when using the gfm format. This feature appears to have been removed in c4af1a1bed2cf448cb4e10d0d0dcae246a8c0b5e.
This breaks several mermaid functionalities, such as being able to use nodes in the diagram to link to other sections in the document -- shown in Figures 1 and 2.
Why was this feature removed in c4af1a1bed2cf448cb4e10d0d0dcae246a8c0b5e? Can it be parameterised so I have the option of not turning it into a PNG? Or at least allow me to turn it into an SVG?
Kind regards,
Robrecht
---
Example:
<div class="column-page">
<div id="fig-architecture">
<p>
``` mermaid
flowchart LR
Raw[Raw\nreads]
Counts[Raw\ncounts]
SS[Unimodal\nsample]
MS[Unimodal\nmulti-sample]
MM[Multi-modal\nmulti-sample]
Ingestion[/Ingestion/]
Preproc1[/Single-sample\nprocessing/]
Preproc2[/Multi-sample\nprocessing/]
Integration[/Integration/]
Raw --- Ingestion --> Counts --- Preproc1 --> SS --- Preproc2 --> MS --- Integration --> MM
Ingestion -.-|"- Demux.\n- Mapping"| Ingestion
Preproc1 -.-|"- Count QC\n- Doublet calling\n- Ambient RNA\n- Gatekeeper"| Preproc1
Preproc2 -.-|"- Normalisation\n- Feature filtering\n- Feature selection\n- Batch correction?\n- Dim. red.?"| Preproc2
Integration -.-|"- Dim. red.\n- Data integration"| Integration
linkStyle 8,9,10,11 stroke:#fff,stroke-width:0px,text-align:left;
click Ingestion "https://github.com/openpipelines-bio/openpipeline/blob/e1d4e6675f46e10805fc9f5bbc47917e3c16ea64/docs/design.md#ingestion"
```
</p>
Figure 1: Before commit c4af1a1bed2cf448cb4e10d0d0dcae246a8c0b5e. Notice how clicking the 'Ingestion' box takes you to the section documenting the 'Ingestion' pipeline.
</div>
</div>
<div class="column-page">
<div id="fig-architecture">
<p>
<img src="https://raw.githubusercontent.com/openpipelines-bio/openpipeline/e1d4e6675f46e10805fc9f5bbc47917e3c16ea64/docs/design_files/figure-gfm/mermaid-figure-1.png" data-fig-pos="H"
style="width:13.97803in;height:2in" />
</p>
Figure 2: After commit c4af1a1bed2cf448cb4e10d0d0dcae246a8c0b5e. This PNG does not integrate well with a dark themed github and does not allow for linking to other pages.
</div>
</div> | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-05-30T18:00:06Z",
"creator": "rcannood",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1021,
"state": "closed",
"title": "Mermaid in gfm turned into PNG",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1021"
} |
When I try to embed an image with a relative path from a markdown file that exists in a subdirectory as shown below, docx output on Windows seems to fail. (`quarto render --to docx`)
It was not a problem on Linux, so it may be related to the path separator character.
```sh
$ tree .
.
├── img.png
├── _quarto.yml
└── sub
└── test.md
```
test.md's content
```md
---
title: "quarto-test"
---
## Quarto
``` | {
"assignee": "jjallaire",
"comments": 7,
"created_at": "2022-05-30T10:34:50Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "1.0",
"number": 1019,
"state": "closed",
"title": "Cannot find images in relative path on docx book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1019"
} |
*Discovered via <https://github.com/quarto-dev/quarto-web/issues/125>*. I did not know there is `quarto pandoc` and `quarto run`, these commands should definitely be listed at `quarto help`. `quarto run --help` might also be implemented and `quarto pandoc --help` already works by passing help to pandoc executable. | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-30T07:45:19Z",
"creator": "nichtich",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1018,
"state": "closed",
"title": "quarto run and quarto pandoc should be listed as commands in quarto help",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1018"
} |
Using the followinging code, the figure is entitled "Figure 1..." regardless of the number of preceding figures that exist.
Removing the captions "Famous Elephants" destroys the layout. The layout becomes split into two rows.
```markdown
::: {#fig-elephants layout-ncol=2}
{#fig-surus}
{#fig-hanno}
Famous Elephants
:::
``` | {
"assignee": "jjallaire",
"comments": 3,
"created_at": "2022-05-29T17:22:51Z",
"creator": "rccline",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": "1.0",
"number": 1017,
"state": "closed",
"title": "In mulitcolumn layout, figure is named Figure 1 regardless of preexisting named figures. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1017"
} |
It seems the `self-contained` doesn’t work for single HTML generation in the latest update.
To reproduce:
```
---
title: "ggplot2 demo"
author: "Norah Jones"
date: "5/22/2021"
format:
html:
fig-width: 8
fig-height: 4
code-fold: true
self-contained: true
---
## Air Quality
@fig-airquality further explores the impact of temperature on ozone level.
```{r}
#| label: fig-airquality
#| fig-cap: Temperature and ozone level.
#| warning: false
library(ggplot2)
ggplot(airquality, aes(Temp, Ozone)) +
geom_point() +
geom_smooth(method = "loess"
)
```
```
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-29T16:19:36Z",
"creator": "jlduan",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1016,
"state": "closed",
"title": "`self-contained` doesn’t work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1016"
} |
When `aside` is used on a slide with a single figure, there seems a clash between `aside` and `r-stretch`: the figure is stretched too much and the `aside` content overlaps the bottom of the figure. If there is a caption for the figure, the caption even goes below the `aside` content.
Desired behavior is that `aside` contents have priority, and they always take the bottom part of the slide; if a single figure is included, it should be stretched to the top of the `aside` block. Is this something that can be implemented? @cderv
Try the MRE below.
```markdown
---
title: "`aside` class"
format: revealjs
---
## Slide 1
::: {.aside}
Something here. A figure without caption
:::
## Slide 2
::: {.aside}
Something here. A figure with caption
:::
## Slide 3
There is no figure on this slide.
::: {.aside}
`aside` works well.
:::
## Slide 4
::: {layout-ncol=2}
Mix text and figures.
:::
::: {.aside}
`aside` works well.
:::
```
| {
"assignee": "cderv",
"comments": 5,
"created_at": "2022-05-28T20:50:07Z",
"creator": "juliantao",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1013,
"state": "closed",
"title": "[revealjs]: `aside` class",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1013"
} |
Quarto provides a very convenient syntax to customize the [citation](https://quarto.org/docs/authoring/footnotes-and-citations.html#sec-citations) and [reference styles for figures](https://quarto.org/docs/authoring/cross-references.html#references).
It seems that this syntax does not apply to other crossref types such as the sections. An MRE is as follows,
```markdown
---
title: Custom crossref style
number-sections: true
format: html
---
## Section I
Something here.
## Section II {#sec-trial}
Something else. -@sec-trial
```
While I understand that the global print style for the title and references can be [customized in the `yaml` header](https://quarto.org/docs/authoring/cross-references.html#options), thre are times I want to use a customized printout in the text.
Another example is illustrated in the [hackish template I made for the American Society of Civil Engineers (ASCE)](https://github.com/juliantao/asce-quarto). The writing style is shared by 35 different ASCE journals and numerous ASCE proceedings.
An issue is that in the `LaTex` class file, the appendixes are numbered, but the sections in the main text are not. I set the global section reference style to have a prefix of `Section`. When I want to reference for example Appendix I, I wrote `Appendix @sec-something`, and the rendered text becomes `Appendix Section I`, which is expected but not ideal.
So if we can use a syntax such as `Appendix -@sec-somthing`, hopefully, we can get `Appendix I` in the rendered file.
| {
"assignee": null,
"comments": 2,
"created_at": "2022-05-28T20:34:25Z",
"creator": "juliantao",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1012,
"state": "closed",
"title": "Custom crossref style for non-figure references",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1012"
} |
When I run quarto preview on the latest build, favicon does not display correctly. (It seems to be looking for absolute paths)
```sh
$ quarto preview
Preparing to preview
Watching files for changes
Browse at http://localhost:4870/
GET: /
/img/favicon.png (404: Not Found)
```
```yaml
website:
favicon: img/favicon.png
```
v0.9.429 works, and v0.9.471 does not work. | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-28T15:01:47Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1010,
"state": "closed",
"title": "favicon not faund error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1010"
} |
It seems that cross reference links are generated for figures with HTML links even if they are not set.
When two figures like the following are embedded in HTML, hover the cursor over the former and the clip symbol will appear.
```md
[]()
```
 | {
"assignee": null,
"comments": 2,
"created_at": "2022-05-28T14:46:44Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1009,
"state": "closed",
"title": "Generation of links to unintended images",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1009"
} |
I tried the About page (https://quarto.org/docs/websites/website-about.html), but the rendered results seem to be different from those on the reference page.
The reference page shows links like that.
But I get this one (simple linked text).
```yaml
about:
template: marquee
links:
- icon: github
text: GitHub
href: https://github.com/
``` | {
"assignee": "dragonstyle",
"comments": 8,
"created_at": "2022-05-28T13:00:51Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1008,
"state": "closed",
"title": "About page's links are simple link",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1008"
} |
HTML page, the copy button does not appear on the former and the copy button appears on the latter.
````
```shell
ls -a
```
```sh
ls -a
```
````
Do you know by what criteria this difference is occurring? (Or is there a list of names?) | {
"assignee": null,
"comments": 8,
"created_at": "2022-05-28T08:34:02Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1007,
"state": "closed",
"title": "Code blocks not considered code blocks?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1007"
} |
With quarto v0.9.468 doesn't render the banner image.
But I switched to v0.9.429 (from this comment https://github.com/quarto-dev/quarto-cli/issues/95#issuecomment-1131599982), it works. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-28T08:15:00Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1006,
"state": "closed",
"title": "`title-block-banner: <path>` does not work with the latest quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1006"
} |
The mouse selects wrong items on interactive charts for `revealjs` presentations - sometimes interactivity stops working altogether.
The same issue happens on the Presentation window of RStudio, Edge Browser and Chrome - inside Quarto .md file (notebook) interactivity works without issue.
The screenshot shows when clicking the red legend, the blue legend gets selected. When clicking blue legend nothing happens.
**Code to repliate**
`````yaml
---
format:
revealjs:
self-contained: true
incremental: true
transition: convex
slide-number: true
controls: true
controls-layout: edges
---
## Plot and Data {.smaller .scrollable }
::: panel-tabset
### Plot
```{r}
library(echarts4r)
library(htmlwidgets)
library(webshot2)
df <- data.frame(
#x = LETTERS[1:5],
x = c("Sales", "Marketing", "C", "D","E" ),
y = c(0,2,3,4,7),#runif(5, 1, 5),
z = runif(5, 3, 7)
)
radar_chart = df |>
e_charts(x) |>
e_radar(y, max = 7, name = "Quarter 1", color=c("red","blue") )|>
e_radar(z, name = "Quarter 2") #|>
#e_legend(show = FALSE)
radar_chart
```
---
### Data
```{r}
df
```
### tree graph
```{r}
library(tibble)
tree <- tibble(
tibble(name = "earth","fire"), # 1st level
children = list(
tibble(name = c("land", "ocean"), # 2nd level
children = list(
tibble(name = c("forest", "river")), # 3rd level
tibble(name = c("fish", "kelp"),
children = list(
tibble(name = c("shark", "tuna"), # 4th level
NULL # kelp
))
)
))
)
)
tree |>
e_charts() |>
e_tree() |>
e_title("Tree graph")
```
### data
```{r}
tree
```
:::
`````
| {
"assignee": null,
"comments": 3,
"created_at": "2022-05-27T18:17:02Z",
"creator": "rleyvasal",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1004,
"state": "open",
"title": "Mouse hover on interactive graph works on wrong positions on `revealjs` presentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1004"
} |
It would be great if Chalkboard can be used in self-contained slides. One of the great features of presentations is the ability to make notes on the screen and this is not currently possible with self-contained.
I get the following error message when trying to render `revealjs` slides in self-contained mode.
`Reveal plugin 'RevealChalkboard is not compatible with self-contained output`
**Code to replicate**
```yaml
---
format:
revealjs:
self-contained: true
incremental: true
transition: convex
slide-number: true
chalkboard:
buttons: false
---
``` | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-27T17:45:52Z",
"creator": "rleyvasal",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1003,
"state": "closed",
"title": "[Feature Request] Allow RevealChalkboard on self-contained slides `revealjs`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1003"
} |
Discovered working on a prototype quarto version manager https://github.com/dpastoor/qvm following the XDG_CONFIG spec, which puts application stuff in the dir `~/Library/Application Support` on mac
first issue was:
```
quarto render test.qmd
/Users/devin/Library/Application Support/qvm/active/bin/quarto: line 106: /Users/devin/Library/Application: No such file or directory
```
after going and adding quotes in the shell expansion, then got to the next error:
```
quarto render test.qmd
error: Unable to load 'file:///Users/devin/Library/Application' import map
Caused by:
No such file or directory (os error 2)
```
at this point talked to @dragonstyle on slack and he said to file and issue and he'll track it down in due time. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-27T17:12:21Z",
"creator": "dpastoor",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1002,
"state": "closed",
"title": "quarto will error if path for quarto structure has spaces in it (eg quarto exe + shared dirs)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1002"
} |
We're seeing the following error during CI runs on Ubuntu 20.04
https://github.com/mlr-org/mlr3book/runs/6628847525?check_suite_focus=true
```
Error running filter /opt/quarto/share/filters/quarto-pre/quarto-pre.lua:
/opt/quarto/share/filters/quarto-pre/quarto-pre.lua:3417: attempt to index a nil value (local 'f')
stack traceback:
/opt/quarto/share/filters/quarto-pre/quarto-pre.lua:3381: in function </opt/quarto/share/filters/quarto-pre/quarto-pre.lua:3374>
make: *** [Makefile:32: pdf] Error 1
Error: Process completed with exit code 2.
```
Rendering locally using MacTex 2022 works fine.
`quarto` 0.9.466 in both setups. Unfortunately the CI run does not really return helpful error contents.
Any idea what we could try?
The source can be found [here](https://github.com/mlr-org/mlr3book/tree/quarto). Thanks for your help! | {
"assignee": "dragonstyle",
"comments": 13,
"created_at": "2022-05-27T17:02:26Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1001,
"state": "closed",
"title": "`/opt/quarto/share/filters/quarto-pre/quarto-pre.lua:3417: attempt to index a nil value (local 'f')`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1001"
} |
I'm having an issue getting `shiny::downloadButton` to appear in a shiny document through Quarto. I can get `shiny::downloadLink` to correctly appear and download data as expected.
I am on:
* Quarto version 0.9.464
* RStudio 2022.02.1+461 "Prairie Trillium" Release (8aaa5d470dd82d615130dbf663ace5c7992d48e3, 2022-03-17) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
* R version 4.1.3 (2022-03-10)
I tested this with a new Quarto Shiny presentation, with only minor additions. This version has `downloadButton`, which doesn't work, but changing it to `downloadLink` works as expected:
````
---
title: "Test"
format: html
server: shiny
---
## Shiny Documents
This Quarto document is made interactive using Shiny. Interactive documents allow readers to modify parameters and see the results immediately. Learn more about Shiny interactive documents at <https://quarto.org/docs/interactive/shiny/>.
## Inputs and Outputs
You can embed Shiny inputs and outputs in your document. Outputs are automatically updated whenever inputs change. This demonstrates how a standard R plot can be made interactive:
```{r}
sliderInput("bins", "Number of bins:",
min = 1, max = 50, value = 30)
plotOutput("distPlot")
downloadButton(outputId = 'faithfulData')
```
```{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')
})
output$faithfulData <-
downloadHandler(
filename = function() {
paste0('data.csv')
},
content = function(file) {
write.csv(
x = faithful,
file = file
)
}
)
```
```` | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-27T14:19:53Z",
"creator": "AnthonyRaborn",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 999,
"state": "open",
"title": "shiny::downloadButton not appearing in Quarto Shiny document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/999"
} |
When working in a quarto book, I would like to reference a chapter (ideally, having its name and number) which is located in a different file.
Given the following structure
```
_quarto.yml
intro.qmd
python.qmd
```
I would like to reference `python.qmd`into `intro.qmd`, so following [this guide in the official documentation](https://quarto.org/docs/books/book-crossrefs.html#creating-references), I did the following:
In `python.qmd`:
```quarto
# Introduction to Python {#sec_python}
```
and in `intro.qmd`:
```md
# Introduction
This is where I'd like to reference [Chapter -@sec_python]
```
But when I run `quarto preview` or `quarto render` I get the following warning: `[WARNING] Citeproc: citation sec_python not found`
And this is what I can see:
I'm using quarto v.0.9.464
| {
"assignee": "jjallaire",
"comments": 13,
"created_at": "2022-05-27T10:38:20Z",
"creator": "ccamara",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": "1.0",
"number": 1135,
"state": "closed",
"title": "Referencing a book chapter is not working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1135"
} |
I've read #196 and the linked documentation but still do not know how to proceed.
We're currently aiming to switch from a large bookdown book to quarto.
For the PDF output we get errors like
```tex
compilation failed- error
LaTeX Error: Cannot determine size of graphic in ./images/learner.svg (no Bou
ndingBox).
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.1636 \includegraphics{./images/learner.svg}
```
The source references the file via
````r
```{r 02-basics-001, echo = FALSE}
knitr::include_graphics("images/ml_abstraction.svg")
```
````
This works with bookdown but quarto does not seem to take it directly.
Can quarto already handle such cases dynamically? | {
"assignee": null,
"comments": 19,
"created_at": "2022-05-27T08:44:51Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 997,
"state": "open",
"title": "Book: PDF output with SVG images",
"url": "https://github.com/quarto-dev/quarto-cli/issues/997"
} |
Similar to #990, it would be great if one could change top-level colors like `color-bg` for only light or dark theme respectively.
Often enough the default colors (or the adapted ones) don't look great in one theme setting.
E.g. something along the lines of
```yml
format:
html:
theme:
light:
css: [default, custom.scss]
code-color: "blue" # just an example
dark:
css: [custom-dark.scss, slate]
code-color: "red" # just an example
```
Currently these must be changed within a custom `.scss` file though there changes often must make use of the `!important` option to get honored and by this do more than they should do. | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-27T07:56:57Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 996,
"state": "closed",
"title": "Wish: Changing SCSS variables for light/dark themes only",
"url": "https://github.com/quarto-dev/quarto-cli/issues/996"
} |
I was using [scoop](https://scoop.sh/) to install R (via the main bucket), RStudio and Quarto (both via [cderv/r-bucket](https://github.com/cderv/r-bucket)). However, I found a wired issue that RStudio errored when rendering quarto documents saying that:
```
ERROR: Error executing 'C:\Users\hongy\scoop\apps\r\current\bin\Rscript': 系统找不到指定的文件。 (os error 2)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
But directly running `quarto render test.qmd` from command line works.
After some search though the codebase, I found that `rBinaryPath("Rscript")` was called to run `Rscript` with given arguments. `rBinaryPath()` internally uses `QUARTO_R`, `R_HOME` and Windows Registry entry to locate the `bin` directory under the R installation folder. Then use `bin/Rscript.exe` as the target path.
https://github.com/quarto-dev/quarto-cli/blob/af5c051e8251d3a0535f2e8dcf62d011259c8fb2/src/core/run/r.ts#L14-L33
However, this did not work if R was installed via scoop in RStudio. There are several related issues here:
If R was installed via scoop:
1. There is no Windows Register key written
2. The `Rscipt.exe` was only at `bin\x64|x32\Rscript.exe`, and scoop did not create links for `Rscript.exe` under the `bin` folder. See: https://github.com/ScoopInstaller/Main/blob/master/bucket/r.json#L22-L40
3. Shims for `Rscript.exe`, `R.exe`, `Rterm.exe` and etc. were created under `~/scoop/shims`. This folder was added to the user PATH so that every other program can access them. This is why directly running `quarto render` from the command line works. `rBinaryPath("Rscript")` will use the path that `which("Rscript")` returns.
However, when quarto was called in R, since the `R_HOME` environment variable was automatically created. `rBinaryPath("Rscript")` will use `R_HOME/bin/Rscript.exe` which does not exist.
One solution maybe is instead of directly returning `R_HOME/bin/Rscript.exe`:
1. Check if the path exists
2. If not, try testing `R_HOME/bin/{arch}/Rscript.exe` | {
"assignee": "cderv",
"comments": 6,
"created_at": "2022-05-27T06:23:03Z",
"creator": "hongyuanjia",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 995,
"state": "closed",
"title": "Failed to locate `Rscript.exe` if R was installed via scoop in RStudio",
"url": "https://github.com/quarto-dev/quarto-cli/issues/995"
} |
This one is a bit of a doozy. Something is happening with our OJS runtime's es6 import resolver that causes other OJS imports to fail silently if we specifically attempt to import d3 from skypack inside one of the JS sources.
The failure doesn't happen if we import _other_ libraries from skypack...
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-05-27T04:45:46Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"invalid",
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 994,
"state": "closed",
"title": "importing d3 from skypack in JS imports from OJS breaks the rest of OJS",
"url": "https://github.com/quarto-dev/quarto-cli/issues/994"
} |
When having a Non ascii accout name in Windows system, for example `echo %username%` in CMD list a Chinese Account name, run `quarto render hello.ipynb --to html` will give an error:
```
Error running filter C:/quarto-0.9.446-win/share/filters/quarto-pre/quarto-pre.lua:
...arto-0.9.446-win/share/filters/quarto-pre/quarto-pre.lua:3420: attempt to index a nil value (local 'f')
stack traceback:
...arto-0.9.446-win/share/filters/quarto-pre/quarto-pre.lua:3384: in function <...arto-0.9.446-win/share/filters/quarto-pre/quarto-pre.lua:3377>
```
Pandoc has no problem. `pandoc hello.ipynb -o hello.html` is ok.
Quarto Version: 0.9.446 | {
"assignee": "dragonstyle",
"comments": 10,
"created_at": "2022-05-27T04:06:04Z",
"creator": "jinlin82",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 993,
"state": "open",
"title": "error because of Non ascii account name in Windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/993"
} |
I have Rstudio running as a workstation and as Rstudio server on (the same) Ubuntu 20 laptop. Current version of Rstudio, markdown, tinytex, quarto. I can generate PDFs from Rmarkdown and Quarto in Rstudio workstation, but attempts to generate PDFs from Rstudio Server fail with:
```
compilation failed- no matching packages
LaTeX Error: File `scrartcl.cls' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: cls)
Enter file name:
! Emergency stop.
<read *>
l.10 \usepackage
{amsmath,amssymb}
```
I would welcome suggestions for fixing this.
| {
"assignee": null,
"comments": 7,
"created_at": "2022-05-27T01:09:05Z",
"creator": "aetiologicCanada",
"is_pull_request": false,
"labels": [
"latex"
],
"locked": false,
"milestone": "Future",
"number": 992,
"state": "closed",
"title": "Quarto, Rstudio server and Latex library",
"url": "https://github.com/quarto-dev/quarto-cli/issues/992"
} |
When you define two themes, one light and one dark. It shows a button for switching light and dark, which is very good.
However, if you choose the dark mode and switch between different pages, chapters or sections. The website is flashing to the light mode first and change to dark theme. It is obvious and easily noticed.
I don't know the reason, but Hugo website do not have this issue. Quarto is great and I really like it, hope it better. Thanks. | {
"assignee": null,
"comments": 6,
"created_at": "2022-05-26T23:34:05Z",
"creator": "wenyaoliu",
"is_pull_request": false,
"labels": [
"early-in-release"
],
"locked": false,
"milestone": "v1.4",
"number": 1325,
"state": "open",
"title": "Flashing when switching between pages in dark theme. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1325"
} |
Hi! The code bellow works just fine but it seems to be rendering as a string sign when it should be a transpose sign.
This problem also occurs on Rstudio IDE (at VS Code it did not happen).
| {
"assignee": null,
"comments": 5,
"created_at": "2022-05-26T22:45:33Z",
"creator": "Gabrielforest",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 991,
"state": "closed",
"title": "Julia transpose operator not rendering properly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/991"
} |
AFAICS one can currently only set one highlighting theme.
It would be great if one could select one for each, light and dark mode. Light highlighting themes are not easy on the eyes in dark website themes 🙂
I am aware that some styles exists which provide light and dark themes - however selecting different ones for light and dark would be great! | {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-05-26T20:04:12Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 990,
"state": "closed",
"title": "Different syntax highlighting theme for light/dark modes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/990"
} |
Many thanks for creating this wonderful `quarto` package. I have switched [my blog](https://www.shamindras.com/posts.html) from [`distill`](https://rstudio.github.io/distill/blog.html) to quarto.
I wanted to setup an RSS feed per the [quarto instructions](https://quarto.org/docs/websites/website-blog.html#rss-feed). Since my main [`index.qmd`](https://github.com/shamindras/ss_personal_quarto_blog/blob/main/index.qmd) is a title page, and my blog posts are contained in a separate [`posts.qmd`](https://github.com/shamindras/ss_personal_quarto_blog/blob/main/posts.qmd) file, I added the `feed : true` change in the `posts.qmd` file instead of the `index.qmd`, as seen [here](https://github.com/shamindras/ss_personal_quarto_blog/blob/main/posts.qmd#L10). I then added in [this line](https://github.com/shamindras/ss_personal_quarto_blog/blob/main/_quarto.yml#L25-L26) in `_quarto.yml`.
However the [rendered RSS feed](https://www.shamindras.com/index.xml) gives a `404 Error`. Is there a way for me to get this working for my blog given my setup? | {
"assignee": null,
"comments": 4,
"created_at": "2022-05-26T19:04:27Z",
"creator": "shamindras",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 989,
"state": "closed",
"title": "Link RSS feed from `posts.qmd` rather than `index.qmd`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/989"
} |
It looks like there’s some bad interaction between `page-layout: full`, our two-column setup, and `code-tools: true`. Evidence:
- the bootstrap buttons in [this page](https://quarto.org/docs/interactive/ojs/examples/layout.html
) don't work.
- the bootstrap buttons in [this page](https://quarto.org/docs/interactive/ojs/examples/penguins.html) _do_ work.
- if we take the `layout.qmd` file that generates the first page and render it outside of a website (so we don't get a two-column layout), then the buttons work again.
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-26T16:30:36Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 987,
"state": "closed",
"title": "`page-layout: full`, our two-column setup, and `code-tools: true` interact badly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/987"
} |
I just installed quarto for the first time and am just trying to run through the "getting started" example, but I immediately hit an error when trying to render the document. I am able to open the ipynb document that's created with jupyter and run that without any issues.
> quarto check jupyter
[✓] Checking Python 3 installation....OK
Version: 3.6.3 (Conda)
Path: /Users/smc77/anaconda/bin/python
Jupyter: 4.9.1
Kernels: python3, ir, python2
(\) Checking Jupyter engine render....
isinstance() arg 2 must be a type or tuple of types
[IPKernelApp] WARNING | Parent appears to have exited, shutting down.
[✓] Checking Jupyter engine render....OK
Similarly, when I try to render a simple test document, I get:
> quarto render test.qmd --to html
ERROR:
isinstance() arg 2 must be a type or tuple of types
| {
"assignee": null,
"comments": 2,
"created_at": "2022-05-26T14:56:49Z",
"creator": "smc77",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 985,
"state": "closed",
"title": "jupyter python3 error: isinstance() arg 2 must be a type or tuple of types?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/985"
} |
The description on book publishment online is quite confussing
See https://quarto.org/docs/books/https://quarto.org/docs/books/#publishing
Please do not refer to the deployment of website if there are difference. The website recommend output-dir to be **docs**, and saying deploy the output files to github. In fact, it should upload the whole resp online and set the page directory to docs. What's worse, the book publishment, recommended output-dir to be **_book** while saying the website is recommending output at **_site**
All together, Confusing !!! | {
"assignee": null,
"comments": 0,
"created_at": "2022-05-26T04:27:28Z",
"creator": "wenyaoliu",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1322,
"state": "closed",
"title": "Publish of book is quite confusion",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1322"
} |
These two fenced divs
````
:::{#my_id}
text
:::
:::{.callout-note #my_id}
text
:::
````
produce these HTML fragments:
```
<div id="my_id">
<p>text</p>
</div>
```
```
<div class="callout-note callout callout-style-default callout-captioned">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
<i class="callout-icon"></i>
</div>
<div class="callout-caption-container flex-fill">
Note
</div>
</div>
<div id="my_id" class="callout-body-container callout-body">
<p>text</p>
</div>
</div>
```
In the first case, the id is inserted into the div tag but in the second it is not included in the outer div. This is not what I expect according the guidelines on fenced divs in the pandoc manual (https://pandoc.org/MANUAL.html#extension-fenced_divs).
Would it be possible to incorporate id values (even in callouts) into the outer div? This would allow for further customization using the id value.
| {
"assignee": null,
"comments": 2,
"created_at": "2022-05-25T19:44:01Z",
"creator": "rich-iannone",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 982,
"state": "closed",
"title": "Fenced div doesn't allow insertion of `id` when using a `callout` class",
"url": "https://github.com/quarto-dev/quarto-cli/issues/982"
} |
When the [`fig-column`, `column`](https://quarto.org/docs/reference/cells/cells-knitr.html#page-columns) or [`classes`](https://quarto.org/docs/reference/cells/cells-knitr.html#attributes) chunk option is set to one of Quarto's [predefined article layout classes](https://quarto.org/docs/authoring/article-layout.html#available-columns), it does not get applied to htmlwidgets (or their surrounding HTML divs respectively).
Consider the following reproducible example:
- Source file: [`test.qmd`](https://salim-b.gitlab.io/adhoc/test.qmd)
- Render command: `quarto render test.qmd --to=html -M keep-md:true`
- Intermediate Markdown file: [`test.md`](https://salim-b.gitlab.io/adhoc/test.md)
- Final HTML file: [`test.html`](https://salim-b.gitlab.io/adhoc/test.html)
OTOH, wrapping the code chunk that contains the htmlwidget in a Pandoc div with the desired layout class works fine (as long as you set `echo: false` since the input code `<pre>` element would also get the full screen width):
````rmd
::: {.column-screen}
```{r}
#| label: fig-widget
#| fig-cap: "An htmlwidget figure"
#| out-width: 100%
#| echo: false
plotly::plot_ly(data = cars,
type = "scatter",
mode = "markers",
x = ~speed,
y = ~dist)
```
:::
````
---
The resulting HTML div structure with the chunk option `fig-column: screen` set is...
```html
<div class="cell fig-column-screen">
...
<div id="fig-widget" class="quarto-figure quarto-figure-center anchored">
<figure class="figure">
<div id="htmlwidget-..." style="width:100%;height:480px;" class="plotly html-widget"></div>
<script type="application/json" data-for="htmlwidget-...">...</script>
<p></p>
<figcaption aria-hidden="true" class="figure-caption">Figure 2: An htmlwidget figure</figcaption>
<p></p>
</figure>
</div>
</div>
```
(for chunk option `column: screen`, the first line above shrinks to `<div class="cell">`)
...whereas correct would be:
```html
<div class="cell page-columns page-full"> <!-- CHANGED -->
...
<div class="cell-output-display column-screen"> <!-- ADDED -->
<div id="fig-widget" class="quarto-figure quarto-figure-center anchored">
<figure class="figure">
<div id="htmlwidget-..." style="width:100%;height:480px;" class="plotly html-widget"></div>
<script type="application/json" data-for="htmlwidget-...">...</script>
<p></p>
<figcaption aria-hidden="true" class="figure-caption">Figure 2: An htmlwidget figure</figcaption>
<p></p>
</figure>
</div>
</div> <!-- ADDED -->
</div>
```
With the workaround, the resulting structure is in contrast:
```html
<div class="column-screen">
<div class="cell">
...
<div id="fig-widget" class="quarto-figure quarto-figure-center anchored">
<figure class="figure">
<div id="htmlwidget-e5ae17d1cb7fb9ba5e0f" style="width:100%;height:480px;" class="plotly html-widget"></div>
<script type="application/json" data-for="htmlwidget-e5ae17d1cb7fb9ba5e0f">...</script>
<p></p>
<figcaption aria-hidden="true" class="figure-caption">Figure 2: An htmlwidget figure</figcaption>
<p></p>
</figure>
</div>
</div>
</div>
```
| {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2022-05-25T17:07:08Z",
"creator": "salim-b",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 981,
"state": "closed",
"title": "`fig-column`, `column` or `classes` chunk options have no effect for htmlwidgets",
"url": "https://github.com/quarto-dev/quarto-cli/issues/981"
} |
it appears that the `background-image` is never embedded in the `html` file for some reason.
If the background image is set with `{background-image="assets/background.jpg"}`, it is embedded.
The following setup in the yaml, will result in slides without background.
While, it's working fine when the generated `html` is at the same level as the `qmd` file it comes from.
```
format:
revealjs:
self-contained: true
background-image: background.jpg
output-file: docs/index.html
```
The image path is not replaced by a the `base64` version of the image.
From the HTML file generated:
```html
// Parallax background image
parallaxBackgroundImage: 'background.jpg',
```
Example: https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli%23980
Version: `0.9.449`
Originally from: quarto-dev/quarto-cli#951
| {
"assignee": null,
"comments": 2,
"created_at": "2022-05-25T16:16:10Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "Future",
"number": 980,
"state": "open",
"title": "`background-image` not embedded when `embed-resource: true` ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/980"
} |
Hi Team Quarto,
I've been using the Quarto engine to generate a website and blog posts for months but just encountered the following error for the first time when attempting to render:
```
ERROR: TypeError: Cannot read properties of undefined (reading 'innerHTML')
```
This is triggered by the `blog.qmd` which has the following content:
```
---
title: "Blog"
listing:
contents: posts
sort: "date desc"
type: default
categories: true
---
```
I was able to replicate this issue on both `0.9.449` and `0.9.446` but going back to `0.9.418` works fine.
zach cp | {
"assignee": "dragonstyle",
"comments": 36,
"created_at": "2022-05-25T15:35:41Z",
"creator": "zachcp",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 979,
"state": "closed",
"title": "New Rendering Error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/979"
} |
Example:
```
---
format: revealjs
---
# Text 1
## Text 2
Text.
::: {.fragment}
### Text 3
Text.
:::
## Final Text
Text.
```
You can't see the final slide as it loops back to the starts after Text 3. | {
"assignee": null,
"comments": 15,
"created_at": "2022-05-25T14:10:55Z",
"creator": "zareami10",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 976,
"state": "closed",
"title": "Putting h(3) in a fragment causes a loop in reveal.js",
"url": "https://github.com/quarto-dev/quarto-cli/issues/976"
} |
Bookdown's `bs4_book` format [supports a `repo.subdir`configuration option](https://bookdown.org/yihui/bookdown/html.html#specifying-the-repository), allowing to specify a path relative to the Git repo given in the `repo.base` config option.
Adding support for a similar Quarto config option **`repo-subdir`** in addition to the existing `repo-url` and `repo-branch` options for website/book projects would accommodate use cases where the actual Quarto project files are stored in a subdirectory of a (bigger) Git repository. | {
"assignee": null,
"comments": 6,
"created_at": "2022-05-25T13:39:40Z",
"creator": "salim-b",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 975,
"state": "closed",
"title": "Add `repo-subdir` config option for website/book projects",
"url": "https://github.com/quarto-dev/quarto-cli/issues/975"
} |
Hi, I am having trouble using mermaid engine on rstudio workbench. I get the error
ERROR: Couldn’t find open server’
I am using quarto 0.9.449 on a linux server and this is my code test
````{mermaid}
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
``` `
Any help much appreciated. | {
"assignee": "cscheid",
"comments": 9,
"created_at": "2022-05-25T13:37:48Z",
"creator": "quinfer",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "1.0",
"number": 974,
"state": "closed",
"title": "mermaid diagram not rendering",
"url": "https://github.com/quarto-dev/quarto-cli/issues/974"
} |
Currently, there's no way to tell which "tab" is active in the main navbar. This should be somehow identifiable (e.g. bold or different color). | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-05-25T13:10:19Z",
"creator": "batpigandme",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1321,
"state": "closed",
"title": "Make active tab/section distinguishable in navbar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1321"
} |
Currently it seems that Chrome is required to render files that contain mermaid.
I think it is guaranteed that Windows has Microsoft Edge installed, so it would be useful to be able to use Microsoft Edge instead of Chrome.
https://github.com/quarto-dev/quarto-cli/blob/cc5119e1c657ed0e11fc2a32ab46559062167113/src/core/puppeteer.ts#L201-L226 | {
"assignee": "cderv",
"comments": 6,
"created_at": "2022-05-25T09:13:13Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 972,
"state": "closed",
"title": "Use Microsoft Edge for rendering (on Windows)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/972"
} |
I recently discovered the [`width` special](https://github.com/observablehq/stdlib/blob/main/README.md#width) included with the OJS standard library! And here I've been, manually sizing my charts like a chump 😛
This isn't necessarily an issue - I would class it more as "surprising behaviour - but `${width}` appears not to be the local width of the chunk in which it is called, but instead appears to be a global variable whose value depends on the location of the chunk in which it is first evaluated.
There might be a race condition here with regard to exactly which chunk that is, but I'm not 100% sure.
Since Observable Notebooks typically run in an environment where all cells have the same width (on <https://observablehq.com>), I'm not entirely surprised that this hasn't come up before! But it could lead to unexpected or surprising results in a Quarto document context.
## Sample A: not called in any OJS chunk (only interpolated into Markdown)
```
---
title: "Test width"
---
The width of this section is **${width}**.
```
Here, `${width}` doesn't evaluate at all. I'm speculating that if no OJS cell is defined then maybe the standard library isn't loaded at all, since even regular string interpolation (eg. `${1+1}`) isn't evaluated.
## Test B: calling in a single OJS chunk
````
---
title: "Test width"
---
Let's see if we detect width!
The width of this section is **${width}**.
## In an OJS block
```{ojs}
md`Width is **${width}**`
```
````
Here, `${width}` evaluates to the width of the section it's called in (_not_ the width of the entire page). it responds as I expect to page-resizing, getting smaller as I shrink the section but maxxing out at the max section width.
## Test C: calling in two OJS chunks of different widths
````
---
title: "Test width"
---
Let's see if we detect width!
The width of this section is **${width}**.
## In an OJS block
```{ojs}
md`Width is **${width}**`
```
And what about in a screen-width section?
::: {.column-screen style="background-color:#ccddff"}
```{ojs}
md`The width of this screen-wide section is **${width}**.`
```
:::
````
Here, _both_ calls of `${width}` refer to the width of the screen section, even though the first call is still in the narrower section. As I resize the page, it responds to the changing size of the screen section. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-05-25T07:23:57Z",
"creator": "jimjam-slam",
"is_pull_request": false,
"labels": [
"enhancement",
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 970,
"state": "closed",
"title": "OJS `width` variable evaluates in surprising ways",
"url": "https://github.com/quarto-dev/quarto-cli/issues/970"
} |
I'm trying to import a `.css` file using the `css` format option in a RStudio project.
The following works:
```
---
format:
html:
css: styles.css
---
```
or
```
---
format:
html:
css: some_dir/styles.css
---
```
However, importing the `.css` file from a parent directory does not seem to work:
```
---
format:
html:
css: ../styles.css
---
```
Currently using Quarto v. 0.9.440 in RStudio v. 4.2.0. | {
"assignee": null,
"comments": 3,
"created_at": "2022-05-25T07:15:07Z",
"creator": "arnaudgallou",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 969,
"state": "closed",
"title": "Importing `.css` from parent directory not working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/969"
} |
rmarkdown support Pandoc `md_extensions` option, does quarto support it yet? | {
"assignee": null,
"comments": 2,
"created_at": "2022-05-25T06:28:40Z",
"creator": "jinlin82",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 968,
"state": "closed",
"title": "md_extensions support?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/968"
} |
When the math rendering method is set to katex, and there is Jupyter widget-like content (e.g. displaying a pandas dataframe in rich format), then math equations cannot be rendered. An example file is katex.ipynb in the zip file. This is the html output:
It seems that the injection of require.js affects the loading of katex.js. As a workaround, modify the generated html file to add a <script> tag of katex.js without defer="" before the <script> tag of require.js.
```html
<!-- existing content before the script tag of loading require.js -->
<!-- add a script tag of loading katex.js without defer="" -->
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/katex.min.js"></script>
<!-- existing content of the script tag of loading require.js -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" integrity="sha512-c3Nl8+7g4LMSTdrm621y7kf9v3SDPnhxLNhcjFJbKECVnmZHTdo+IRO05sNLTH/D3vA6u1X32ehoLC7WFVdheg==" crossorigin="anonymous"></script>
```
[katex.zip](https://github.com/quarto-dev/quarto-cli/files/8767304/katex.zip)
| {
"assignee": null,
"comments": 2,
"created_at": "2022-05-25T01:59:12Z",
"creator": "kendrewlau",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 967,
"state": "closed",
"title": "Katex cannot be loaded with Jupyter widget-like content",
"url": "https://github.com/quarto-dev/quarto-cli/issues/967"
} |
For example, I have a windows batch file: `qmd-html.bat`
```
quarto render %1 --to html
echo %1
pause
```
when i run `qmd-html.bat "hello.ipynb"` in CMD
the first line `quarto render %1 --to html` is fine, but the lines after it don't execute.
System: Windows 7 64bit | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-05-25T01:11:28Z",
"creator": "jinlin82",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 966,
"state": "closed",
"title": "commands after 'quarto render' line don't execute in Windows batch file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/966"
} |
Hello,
I tried to reproduce the quarto documentation ojs examples with the penguins dataset (I'm using VS Code). If I try to load the dataset from a csv file like in the example, it work but if I try to load the dataset with the R packages and to sent it to ojs with the ojs_define() function it doesn't.
To understand why, I tried to simply use ojs to show a table in the rendered document with the next code.
```{r}
library(palmerpenguins)
library(tidyverse)
ojs_define(data2 = as.matrix(penguins, dimnames(list(rownames(penguins),
colnames(penguins))), rownames.force = T))
```
```{ojs}
Inputs.table(data2)
```
I found 2 problems:
1. when I try to use the ojs_define function with a dataframe or a tibble, the ojs cell only give an error; "OJS Error TypeError: e is not iterable".
2. When I try to use the previous code (I convert the dataframe to a matrix), the table show by ojs doesn't keep the columns names.
May I ask you, if there is a solution to this problem. Also, would it be possible that you add on your website a list of the data format that can be sent to ojs and their correspondant javascript format (with more R examples please 🙏 ).
Thank you in advance.
| {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-05-24T14:44:44Z",
"creator": "Pierre9344",
"is_pull_request": false,
"labels": [
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 962,
"state": "closed",
"title": "ojs_define doesn't work well with R dataframe and matrix",
"url": "https://github.com/quarto-dev/quarto-cli/issues/962"
} |
We've definitely made progress. The image URLs all have backslashes now as expected and the index.xml file now passes muster on the SimplePie RSS feed check. Great!
However, the link in the citation at the bottom of the post has forward slashes. Here's the example citation from [https://github.com/graphdr/quarto-forwardslash-reprex](https://github.com/graphdr/quarto-forwardslash-reprex)
```
<div class="quarto-appendix-secondary-label">For attribution, please cite this work as:</div>
<div id="ref-malloc2022" class="csl-entry quarto-appendix-citeas">
Harlow Malloc. 2022.
<span>“Post With Code.”</span>
May 22, 2022.
<a href="https://graphdr.github.io/quarto-forwardslash-reprex/posts\post-with-code">
https://graphdr.github.io/quarto-forwardslash-reprex/posts\post-with-code</a>.
</div>
``` | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-24T13:35:27Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 960,
"state": "closed",
"title": "Windows path separators appearing in appendix urls",
"url": "https://github.com/quarto-dev/quarto-cli/issues/960"
} |
The documentation in [pandoc-user-guide.qmd](https://raw.githubusercontent.com/quarto-dev/quarto-gallery/main/articles/pdf/pandoc-user-guide.qmd) states that
> `xelatex` uses `polyglossia` (with `lang`)
but when using `pdf-engine: lualatex`, `babel` seems to be used by default.
I need to use `polyglossia` with `lualatex` but there seems to be no option for that. | {
"assignee": null,
"comments": 2,
"created_at": "2022-05-24T12:16:26Z",
"creator": "tpellard",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 959,
"state": "closed",
"title": "Using `polyglossia` with LaTeX engines other than xelatex",
"url": "https://github.com/quarto-dev/quarto-cli/issues/959"
} |
Setting `number-sections:true` with pdf as output format breaks the output.
For example:
```
---
title: "My document"
format:
pdf:
toc: true
number-sections: false
---
# Beginning
# Middle
# End
```
The example above works as expected, but as soon as `number-sections` is set to `true`, the created PDF has "End" as Title, and only a single headline with "Table of contents" as content. I tried out several of the previous versions, none of them produced the expected outcome.
With `number-sections:true`, I checked with `keep-tex: true` the `.tex`-file, which had the following as document body:
```
\begin{document}
\maketitle
\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[boxrule=0pt, frame hidden, sharp corners, interior hidden, borderline west={3pt}{0pt}{shadecolor}, enhanced, breakable]}{\end{tcolorbox}}\fi
\renewcommand*\contentsname{Table of contents}
{
\hypersetup{linkcolor=}
\setcounter{tocdepth}{3}
\tableofcontents
}
\end{document}
```
I guess this is a bug in quarto? | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-05-23T18:30:14Z",
"creator": "sknauff",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 956,
"state": "closed",
"title": "`number-sections:true` breaks pdf output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/956"
} |
I've set up a quarto book on github pages with a category listing: https://jamespeapen.github.io/journals/. The category labels are created and are clickable from the home `index.html` page, but not from their individual tags in each book page([like on this page](https://jamespeapen.github.io/journals/src/epigenetics/interplay_between_cancer_genome_epigenome.html)) on the github website. But if I use `quarto preview` locally the tags are clickable. It looks like they have links only with `quarto preview`:
Github pages:
```html
<div class="quarto-categories">
<div class="quarto-category">cancer genomics</div>
<div class="quarto-category">epigenetics</div>
<div class="quarto-category">intro</div>
</div>
```
With quarto-preview:
```html
<div class="quarto-categories">
<div class="quarto-category"><a href="/index.html#category=cancer%20genomics">cancer genomics</a></div>
<div class="quarto-category"><a href="/index.html#category=epigenetics">epigenetics</a></div>
<div class="quarto-category"><a href="/index.html#category=intro">intro</a></div>
</div>
```
The [`listings.json`](https://github.com/jamespeapen/journals/blob/gh-pages/docs/listings.json) file is created by the github action.
Here is the workflow I use:
```yaml
on:
push:
branches: main
pull_request:
branches: main
# to be able to trigger a manual build
workflow_dispatch:
name: Render and deploy Book
jobs:
build-deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Install Quarto
uses: quarto-dev/quarto-actions/install-quarto@v1
- name: Build book
run: |
git config --global user.name "${GITHUB_ACTOR}"
git config --global user.email "${GITHUB_ACTOR}@users.noreply.github.com"
git checkout -b gh-pages
quarto render --to html
git add docs
cid=$(git rev-parse --short "$GITHUB_SHA")
git commit -am "Deploy $cid to gh-pages"
git push origin HEAD:gh-pages --force
``` | {
"assignee": null,
"comments": 7,
"created_at": "2022-05-23T13:31:02Z",
"creator": "jamespeapen",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 953,
"state": "closed",
"title": "Clickable categories not working on github pages - only in local `quarto preview`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/953"
} |
Hello,
I have a problem to render html widget inside tabset. I tried to create venn diagram with the upsetjs package but only the venn in the first (sometime first two) tab is rendered.
I have the same problem with html widget generated by the scatterD3 package.
If I remove the ::: panel-tabset the plot are rendered normally. Any idea of what is the problem and how to resolve it?
I have a qmd file and the rendered page that show the problem:
[test.zip](https://github.com/quarto-dev/quarto-r/files/8753033/test.zip)
Also, do you have any idea of when it willbe possible to use ojs in RStudio?
Thank you in advance for your help.
| {
"assignee": null,
"comments": 1,
"created_at": "2022-05-23T08:58:04Z",
"creator": "Pierre9344",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1076,
"state": "open",
"title": "tabset doesn't seem to work well with html widget",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1076"
} |
Figures are generated in the directory in which the `.qmd` lives.
But in the context of a self-contained HTML, when including `.qmd` files from a subdirectory, images are not retrieved by the main document: `[WARNING] Could not fetch resource content/index_files/figure-html/fig2-1.png`
I tried setting `execute-dir: project`, but same result, _i.e._, the figure from the included `.qmd` is not found.
I found nothing in <https://quarto.org/docs/authoring/includes.html>, but I might have missed something.
```
quarto-cli#951
├── content
│ └── fig2.qmd
└── index.qmd
```
````
---
title: 'quarto-dev/quarto-cli#951'
author: Mickaël Canouil, *Ph.D.*
format:
html:
self-contained: true
---
## Figure
```{r}
#| label: fig1
plot(2)
```
{{< include content/fig2.qmd >}}
````
Example: <https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli%23951>
Version: `0.9.433` | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-05-22T11:06:15Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 951,
"state": "closed",
"title": "Generated figures from an included `.qmd` are not found",
"url": "https://github.com/quarto-dev/quarto-cli/issues/951"
} |
Creating citations for packages from R with `knitr` generates bib entries of the form:
```
@manual{R-knitr,
type = {Manual},
title = {Knitr: {{A}} General-Purpose Package for Dynamic Report Generation in r},
author = {Xie, Yihui},
year = {2020}
}
```
using: `knitr::write_bib(.packages(), "packages.bib")`, see https://bookdown.org/yihui/rmarkdown-cookbook/write-bib.html.
According to this: "There are two possible types of citation entries. One type is generated from the package’s DESCRIPTION file, and the other type is generated from the package’s CITATION file if provided. For the former type, the citation keys are of the form R-pkgname, where pkgname is the package name (e.g., R-knitr). For the latter type, the keys are created by concatenating the package name and the publication year (e.g., knitr2015)."
But it seems that bib-keys prefixed with `...-` can not be used in quarto, which excludes package citations for packages that don't contain a CITATION file but only a DESCRIPTION.
```
See @knuth84, See. @R-knitr
```
Any citation key containing a dash is not recognized.
I assume quarto doesn't allow underscores here as to not clash with `fig-` `sec-` and the likes. Would it make sense to make an exception for `R-`?
| {
"assignee": "dragonstyle",
"comments": 9,
"created_at": "2022-05-22T08:42:08Z",
"creator": "jmbuhr",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 950,
"state": "closed",
"title": "R-package citations can not be found",
"url": "https://github.com/quarto-dev/quarto-cli/issues/950"
} |
As documented on the website (<https://quarto.org/docs/authoring/figures.html#figure-alignment>):
> Figures and their captions are center aligned by default.
But this is currently not true:
- When a figure has a caption, the figure is center aligned, but not the caption.
- When a figure has no caption, the figure is left aligned.
This is consistent for both `html` and `revealjs` formats.
Example: <https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli%23949>
Version: `0.9.433` | {
"assignee": null,
"comments": 4,
"created_at": "2022-05-22T08:39:20Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 949,
"state": "closed",
"title": "Figures left aligned (discrepancy with docs / bug?)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/949"
} |
The following markdown code displays `::: {.cell}` `:::` tag, at least for `html` and `revealjs` format
```md
1. Expliquer les relations entre `a`, `b`, `d` et `e`.
```{r}
#| echo: true
#| eval: false
a <- 1:10
b <- a
b -> e
e <- d <- 1:10
```
```
```md
1. Expliquer les relations entre `a`, `b`, `d` et `e`.
::: {.cell}
```{r}
#| echo: true
#| eval: false
a <- 1:10
b <- a
b -> e
e <- d <- 1:10
```
:::
```
To note, using `.r` works as expected.
Example: https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli%23948
Version: `0.9.433` | {
"assignee": null,
"comments": 4,
"created_at": "2022-05-22T08:07:46Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 948,
"state": "closed",
"title": "Code cells \"tags\" displayed when indented (items list)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/948"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/944
<div type='discussions-op-text'>
<sup>Originally posted by **ManuelSpinola** May 20, 2022</sup>
Does quarto file with shiny work in a quarto project with a yaml?
I tried to run the Old Faithful example but I got the error:
ERROR: Internal Error: getYamlIntelligenceResource called with missing resource schema/project.yml</div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-05-20T22:22:39Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 945,
"state": "closed",
"title": "quarto file with shiny in a quarto project",
"url": "https://github.com/quarto-dev/quarto-cli/issues/945"
} |
While trying to compile any file using a python jupyter kernel, the CLI returns a kernel error.
Example file `hello.qmd`:
```
---
title: "Hello world"
format:
html:
code-fold: true
jupyter:
python3
---
This is a test file.
```
Output from the command `quarto render hello.qmd --to html --log-level info`:
```
Starting python3 kernel...ERROR:
Kernel died before replying to kernel_info
```
.ipynb files run fine on jupyterlab on the same PC, and compiling .qmd files with the R kernel `ir` with jupyter doesn't produce any errors, so I'm not sure what the issue is. | {
"assignee": null,
"comments": 6,
"created_at": "2022-05-20T00:46:39Z",
"creator": "zcline91",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 942,
"state": "closed",
"title": "Python jupyter kernel error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/942"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/939
<div type='discussions-op-text'>
<sup>Originally posted by **ggirton** May 19, 2022</sup>
I have made the _quarto yaml that looks like this, for a blog
project:
type: website
website:
title: "mvpblog"
navbar:
right:
- about.qmd
- icon: github
href: https://github.com/
- icon: twitter
href: https://twitter.com
body-footer: |
--- all photos Copyright © 2022 MeMeMe all rights reserved
format:
html:
theme: cosmo
css: styles.css
Then, the stock index.qmd, like this:
---
title: "mvpblog"
listing:
contents: posts
sort: "date desc"
type: default
categories: true
sort-ui: false
filter-ui: false
page-layout: full
title-block-banner: true
---
The result is that the body footer comes out ABOVE the blog entries in the listing (not after them, as I sort of expected).
I know there must be a way for me to set up logging so I can see where in the process my specification of the body footer is going awry. It's even possible that I'm doing everythnig right and there is a bug! (note from me: this has pretty much never happened before, though).
What I lack is an understanding of how to turn on dedbugging instrumentation, so I can get the dedbugs ded. I mean, debugging, but you know what I mean. Does it think it is doing what I think it should be doing, etc. etct.
Thank you, TIA!
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-19T22:57:03Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 941,
"state": "closed",
"title": "IS there a way to diagnose why body-footer is going in above the blog list?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/941"
} |
Quarto version: 0.9.414
According to https://quarto.org/docs/authoring/tables.html#caption-location, the following should not happen. in my unterstanding.
Using in yaml header (root):
- `cap-location: bottom`:
- figures: bottom => OK
- tables: bottom => OK
- `cap-location: margin`:
- figures: margin => OK
- tables: bottom => __WRONG__ (or unexpected)
- `cap-location: top`:
- figures: top => OK
- tables: top => OK
- `tbl-cap-location: bottom`:
- tables: bottom => OK
- `tbl-cap-location: margin`:
- tables: bottom => __WRONG__ (or unexpected)
- `tbl-cap-location: top`:
- tables: bottom => __WRONG__ (or unexpected)
In code cell option: `#| tbl-cap-location: bottom` or `#| tbl-cap-location: margin` have no effect at all in contrast to `fig-cap-location`.
See examples in https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli-938 | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-19T18:41:28Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 938,
"state": "closed",
"title": "`*cap-location` options does not work well for tables",
"url": "https://github.com/quarto-dev/quarto-cli/issues/938"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/931
<div type='discussions-op-text'>
<sup>Originally posted by **bbartholdy** May 19, 2022</sup>
Hi,
I have a quarto document (let's call it *file1.qmd*) where I would like to include a second quarto document (*_file2.qmd*) that contains the following text and inline R code:
```
This is a file to test the execution of includes inline code.
Inline code test: `r version$version.string`
```
In *file1.qmd* I have the shortcode `{{< include _file2.qmd >}}`
When I render *file1.qmd* with quarto (v. 0.9.426) it currently looks like:
>This is a file to test the execution of includes inline code.
>
>Inline code test: `r version$version.string`
I would like it to look like:
>This is a file to test the execution of includes inline code.
>
>Inline code test: R version 4.2.0 (2022-04-22)
Am I doing something wrong or is it currently not possible to include files with inline R code and have the inline code executed?</div>
This is likely our engine detection going wrong after include expansion. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-05-19T14:47:00Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 932,
"state": "closed",
"title": "Include shortcode not rendering inline R code",
"url": "https://github.com/quarto-dev/quarto-cli/issues/932"
} |
ojs_define doesn't work very well for R spatial dataframes. In practice, it is necessary to convert it to geojson (with geojsonsf package) and then pass it as a string. Then, we have to use JSON.parse ([see](https://neocarto.github.io/Quarto/r_ojs.html)). Why not allow directly to pass a spatial dataframe in well formated geojson? Same thing for dataframes. We have to use transpose systematically. Why not convert directly into an array of objects (and not into an object containing arrays) ?
| {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-05-19T12:05:27Z",
"creator": "neocarto",
"is_pull_request": false,
"labels": [
"enhancement",
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 935,
"state": "closed",
"title": "ojs_define for spatial dataframe (sf)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/935"
} |
Here is a minimal working example to reproduce the problem.
Note how the escape codes are not being handled but instead printed literally.
---
format:
revealjs:
code-fold: false
echo: true
jupyter: julia-1.7
---
```{julia}
quote
a = b + c
d = e - f
end
```
This is what the output should look like:
Here is another example that uses the BenchmarkTools package to benchmark a function call:
---
format:
revealjs:
code-fold: false
echo: true
jupyter: julia-1.7
---
```{julia}
using BenchmarkTools
@benchmark rand(100,100)
```
What the output should look like:
| {
"assignee": null,
"comments": 12,
"created_at": "2022-05-19T08:55:51Z",
"creator": "mroavi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 929,
"state": "open",
"title": "Reveal.js with Julia: escape codes are not handled in output of executable code blocks ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/929"
} |
I have noticed some errors concerning the import of libraries. For example, require("bertin") does'nt work in [Quarto](https://quarto.org/docs/tools/rstudio.html). The following error is returned: OJS Error. RequireError$1: invalid module. To import bertin, I have to write: bertin = import('https://cdn.skypack.dev/[email protected]'). However, require("bertin") works in Observable. Within rstudio, preview in Viewer Pane works. Preview in window doesn't work. Similarly, the html file rendered via quarto render works.
Code to reproduce the bug (within an ojs cell).
(ubuntu 22.04, Rstudio 2022.06.0-daily+420, Quarto 0.9.434)
````
```{ojs}
bertin = require("[email protected]")
```
```` | {
"assignee": "cscheid",
"comments": 9,
"created_at": "2022-05-19T08:37:09Z",
"creator": "neocarto",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 943,
"state": "closed",
"title": "OJS Error. RequireError$1: invalid module. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/943"
} |
Recently I have been writing reports using quarto book. I would like to add shiny objects in some of the pages. Based on what I saw in the documentation (https://quarto.org/docs/interactive/shiny/running.html) I can only serve individual documents.
Is there a way to render and serve multiple documents at the same time using quarto book? I have a VM running with a shiny server already. | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-19T06:48:09Z",
"creator": "chronchi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 928,
"state": "closed",
"title": "Serving books with shiny",
"url": "https://github.com/quarto-dev/quarto-cli/issues/928"
} |
I want to apologize in advance for nitpicking.
I think it is quite unconventional that **bold** text has a smaller font size than regular text:
I went through all the variable definitions that can be tweaked from the scss file, but couldn't find how to do this.
So my 2 questions are: 1. could you please show me how to tweak the font size of bold font and 2. wouldn't it make more sense to have both bold and regular text to have the same font size? | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-18T20:10:45Z",
"creator": "mroavi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 927,
"state": "closed",
"title": "Reveal.js: Bold text is smaller than regular text",
"url": "https://github.com/quarto-dev/quarto-cli/issues/927"
} |
Based on https://github.com/quarto-dev/quarto-cli/issues/722 it seems to me that in pdf format the plot should not be rendered in svg.
If I make graphics with `Gadfly`, here the output is svg, and I receive the following error:
```
compilation failed- error
LaTeX Error: Cannot determine size of graphic in ex_files/figure-pdf/fig-parametric-output-1.svg (no BoundingBox).
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
l.210 ...s/figure-pdf/fig-parametric-output-1.svg}
```
`ex.qmd` is my file, and the has the following structure:
````
---
title: "Plots Demo"
author: "Norah Jones"
date: "5/22/2021"
format: pdf
jupyter: julia-1.7
---
## Parametric Plots
Plot function pair (x(u), y(u)).
See @fig-parametric for an example.
```{julia}
#| label: fig-parametric
#| fig-cap: "Parametric Plots"
using Gadfly
p = plot()
push!(p, layer(x=[2,4], y=[2,4], size=[1.4142], color=[colorant"gold"]))
push!(p, Coord.cartesian(fixed=true))
```
```` | {
"assignee": null,
"comments": 2,
"created_at": "2022-05-18T17:22:54Z",
"creator": "AlissonRP",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 925,
"state": "closed",
"title": "Plots rendered in svg format in Julia",
"url": "https://github.com/quarto-dev/quarto-cli/issues/925"
} |
I'm trying to incorporate a {gt} object as a table in a Quarto .qmd document that outputs to PDF.
When I try to add a table caption within a code chunk (using #| tbl-cap: xyz), I get the following error:
> **Package array Error: Illegal pream-token (\caption): `c' used.**
>
> **See the array package documentation for explanation.**
> **Type H <return> for immediate help.**
> **...**
>
> **l.252 \caption**
> **{\label{tbl-test}Results }**
>
> **see Untitled.log for more information.**
This error occurs whether I try to output the {gt} object using only `gt()` AND if I use `as_latex()` afterwards.
Here's a test document:
---
title: "Untitled"
format: pdf
---
## Libraries
```{r}
library(tidyverse)
library(gt)
```
## Fake Data
```{r}
test_data <- tribble( ~a, ~b,
1, 2,
3, 4,
5, 6
)
```
## Table Output
```{r}
#| label: tbl-test
#| tbl-cap: "Results"
test_data |> gt()
```
## Cross-reference
@tbl-test | {
"assignee": "cderv",
"comments": 9,
"created_at": "2022-05-18T16:37:20Z",
"creator": "SEthanMilne",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 924,
"state": "closed",
"title": "Issues using {gt} objects as cross-referenced tables",
"url": "https://github.com/quarto-dev/quarto-cli/issues/924"
} |
I noticed that by default `h1` slides are vertically centered while `h2` slides are top-aligned.
How can I make `h2` slides vertically centered (like `h1` slides)? I've spent hours trying to tweak this but haven't found out how.
I found that this is how you would achieve this using Revealjs's markdown:
```md
<section data-markdown>
<script type="text/template">
<!-- .slide: class="center" -->
Markdown content
</script>
</section>
```
I also found that you can control text-alignment horizontally with the scss theme, e.g.:
```scss
$presentation-slide-text-align: left !default;
```
Thanks in advance! | {
"assignee": null,
"comments": 3,
"created_at": "2022-05-18T15:18:07Z",
"creator": "mroavi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 923,
"state": "closed",
"title": "Vertical alignment using Revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/923"
} |
Consider the following reprex (tested with quarto 0.9.424):
````markdown
---
title: "Table vs. kable"
engine: knitr
---
A Markdown table is *not* striped:
| a| b| c|
|--:|--:|--:|
| 1| 6| 11|
| 2| 7| 12|
| 3| 8| 13|
| 4| 9| 14|
| 5| 10| 15|
But a table generated with `knitr::kable()` is striped (besides other minor differences):
```{r}
data.frame(a=1:5, b=6:10, c=11:15) |> knitr::kable()
```
````
Although the output of the code cell is exactly equal to the Markdown table in the example (the first table), the output look different, most notably only the `kable` is striped:
<img width="869" alt="Screen Shot 2022-05-18 at 16 09 29" src="https://user-images.githubusercontent.com/4377312/169061668-34f3e2d9-ed67-481e-86fe-8db4b02648ec.png">
I would have expected that the tables use the same style by default. If this is not desired, is there a way I can make them the same? | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-18T14:11:00Z",
"creator": "cbrnr",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 922,
"state": "open",
"title": "Markdown tables use different style than code (kable) tables",
"url": "https://github.com/quarto-dev/quarto-cli/issues/922"
} |
As shown in the screenshot，when I create mlr3 learner inRstudio, it can work in chunk. But when I render it, it failed
my project is encoded by UTF-8,but my local is encoded as follow
> Sys.getlocale()
[1] "LC_COLLATE=Chinese (Simplified)_China.936;LC_CTYPE=Chinese (Simplified)_China.936;LC_MONETARY=Chinese (Simplified)_China.936;LC_NUMERIC=C;LC_TIME=Chinese (Simplified)_China.936"
**Setup**
I use
- R version 4.1.3 (2022-03-10) Platform: x86_64-w64-mingw32/x64 (64-bit)
- Quarto v0.9.424
- RStudio 2022.02.2+485 "Prairie Trillium" Release (8acbd38b0d4ca3c86c570cf4112a8180c48cc6fb, 2022-04-19) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
| {
"assignee": null,
"comments": 3,
"created_at": "2022-05-18T13:49:09Z",
"creator": "Damonsoul",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 921,
"state": "closed",
"title": "Rstudio render error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/921"
} |
<img width="405" alt="image" src="https://user-images.githubusercontent.com/20207927/169019697-731f01b1-96c6-4222-a323-47b04f079b5e.png">
<img width="216" alt="image" src="https://user-images.githubusercontent.com/20207927/169019941-50ea82a7-d7fa-49f8-add7-2ea33353261b.png">
The references title in html export is duplicated, while the docx and pdf versions are OK.
| {
"assignee": "dragonstyle",
"comments": 12,
"created_at": "2022-05-18T10:38:10Z",
"creator": "f10w3r",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 920,
"state": "closed",
"title": "Duplicated References Title in html export.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/920"
} |
Does `quarto` support converting custom mime-types to pdf? Maybe something like [preprocessors](https://nbconvert.readthedocs.io/en/latest/nbconvert_library.html#Custom-Preprocessors) in nbconvert?
Currently if I have a custom mime-type it just returns the object type in PDF and Docx formats. | {
"assignee": null,
"comments": 6,
"created_at": "2022-05-18T09:18:21Z",
"creator": "divyansshhh",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 919,
"state": "open",
"title": "Converting custom Mime-Types to PDF and docx",
"url": "https://github.com/quarto-dev/quarto-cli/issues/919"
} |
Downloading the repo and rendering docs/presentations/index.qmd results in:
with in the console:
```js
quarto-ojs-runtime.js:18714 TypeError: Failed to resolve module specifier '....docspresentations
evealjsdemo/./actors.js'
at Interpreter.resolveImportPath (quarto-ojs-runtime.js:18709:19)
at Interpreter.cell (quarto-ojs-runtime.js:11864:38)
at Interpreter.module (quarto-ojs-runtime.js:11838:31)
at runCell (quarto-ojs-runtime.js:19428:40)
at Array.map (<anonymous>)
at QuartoOJSConnector.interpretWithRunner (quarto-ojs-runtime.js:18901:52)
at QuartoOJSConnector.interpret (quarto-ojs-runtime.js:19435:17)
at Object.interpret (quarto-ojs-runtime.js:19670:27)
at Object.interpretFromScriptTags (quarto-ojs-runtime.js:19715:20)
at VM52 title-slide:1705:25
(anonymous) @ quarto-ojs-runtime.js:18714
```
so somehow the importpath seems to get mangled? | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-05-18T07:34:19Z",
"creator": "burgerga",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "Future",
"number": 1320,
"state": "closed",
"title": "Can't get js files in docs/presentations/index.qmd to work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1320"
} |
Is there a chance to get an rpm package as well?
I just converted the deb using `alien` and the resulting rpm works nicely (using the `--scripts` option). Maybe include in a copr?
Edit: tested on Fedora 36, had already installed pandoc and texlive. | {
"assignee": "dragonstyle",
"comments": 9,
"created_at": "2022-05-17T15:30:24Z",
"creator": "TS-CUBED",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 915,
"state": "closed",
"title": "packaging: Release rpm for Fedora/RHEL/...",
"url": "https://github.com/quarto-dev/quarto-cli/issues/915"
} |
I'd like to put notes to a presentation at the end rather than at the foot of each page (i.e., endnotes not footnotes), to avoid distracting the audience.
I see from the yaml [here](https://github.com/quarto-dev/quarto-web/blob/main/docs/authoring/footnotes-and-citations.qmd) that it is possible, at least for html documents, to use the yaml item `footnote-section-title` to create an endnotes section and have the notes appear there. That leads to 4 comments/questions:
1. This doesn't seem to be documented. It would be great to have that. (Happy to do a pull request if the behavior of `footnote-section-title` is not going to change.)
2. It would be nice to be able to control the placement of the footnote (endnote) section, because sometimes it is nice to have such a section appear before an appendix, rather than at the very end. In addition, it would be nice to be able to change its size and formatting so that it conforms with other sections. I don't see a way to do these things. I would much appreciate it if someone could let me know whether these things are possible and if so how.
3. I put `footnote-section-title` in the yaml of a revealjs presentation but it does not create a separate footnotes section. Is it possible to have a footnotes (endnotes) slide in a revealjs (or other) presentation?
4. I note that the yaml referred to above intends to create a section called "Example Footnotes" (first screenshot below) while the web text shows a section called "Footnotes" (second screenshot). It may be that they are out of sync and the published web page has not caught up to the working version of the html yet, which would not be an issue, or it may be that `footnote-section-title` is not doing what it is supposed to do. I think it is the latter because when I create a small example with a named title, it uses "Footnotes" rather than the title I give it.
Intended title is "Example Footnotes":
Actual title is "Footnotes":
| {
"assignee": null,
"comments": 3,
"created_at": "2022-05-17T14:21:53Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 914,
"state": "closed",
"title": "Comments/questions/minor bug re endnotes: (1) feature not documented, (2) would like to format the header, (3) are endnotes possible for presentations?, and (4) footnote-section-title appears not to be working properly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/914"
} |
## Environment
- clean quarto install on Ubuntu Linux (Windows Subsystem, Windows 11)
- clean install `quarto tools install tinytex`
- VS Code with quarto extension
## Reproduce error
- `quarto create-project test-pdf --type book`
- add example code below in `intro.qmd`
- render pdf with VS code extension
- `ERROR: NotFound: No such file or directory (os error 2)`
```
```{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()
```
| {
"assignee": null,
"comments": 6,
"created_at": "2022-05-17T13:37:27Z",
"creator": "dkapitan",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 912,
"state": "closed",
"title": "Rendering pdf for book generates file not found error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/912"
} |
I'm creating a revealjs presentation in RStudio. I would like a bibliography that includes works not referred to in the presentation.
I created a nocite metadata field, as described [here](url). I can insert items manually into the field (e.g., @quarto-2022, or @*) but I cannot insert them using the citation option on the insert dialog. If I put the cursor in the metadata field and then open the dialog, I get the screenshot you see below, with the Citation option greyed out:
 | {
"assignee": null,
"comments": 2,
"created_at": "2022-05-17T13:11:06Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 911,
"state": "closed",
"title": "RStudio visual mode insert-citation option greyed-out when trying to insert citations into a nocite metadata field",
"url": "https://github.com/quarto-dev/quarto-cli/issues/911"
} |
I'm using all latest versions as of now, I believe:
- RStudio-2022.06.0-daily-410.exe
- quarto-0.9.415-win.msi
- Zotero 6.0.7 Windows standalone software
quarto does not see all references in a Zotero folder.
Here's what's in my Zotero folder ("dummy"):
Here's what I get when I use the insert-citation dialog:
You can see that one of the Ron Snell citations does not show.
I am not sure what distinguishes it. However, I created it by hand rather than saving it to the Zotero library through a browser (Chrome) web extension.
The problem does not seem to be on the Zotero end. Here is what I get if I export the dummy subcollection:
It is clearly there in the exported .bib file.
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-17T12:51:12Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 910,
"state": "closed",
"title": "insert-citation dialog in RStudio visual mode does not see all Zotero references",
"url": "https://github.com/quarto-dev/quarto-cli/issues/910"
} |
Once i want a file to be rendered to _pdf_, i get the following error message:
> running xelatex - 1
command xelatex not found, attempting install
finding package for xelatex
> 1 package to install
> installing xelatex (1 of 1)
ERROR: tlmgr returned a non zero status code
TLPDB: not a directory, not loading: /home/kalmer/texmf
tlmgr: running in usermode, did you call `tlmgr init-usertree'? | {
"assignee": "dragonstyle",
"comments": 41,
"created_at": "2022-05-17T12:23:15Z",
"creator": "piiskop",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 909,
"state": "open",
"title": "Rendering to \"pdf\" doesn't work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/909"
} |
From https://github.com/rstudio/rstudio/pull/11201#issuecomment-1128685959
With this R code:
```r
dir.create(tf <- tempfile());
dir.create(file.path(tf, "sub"))
main <- file.path(tf, "main.qmd")
writeLines("---\ntitle: quarto document\n---\n", main)
sub <- file.path(tf, "sub", "sub.qmd")
writeLines("---\ntitle: quarto document\n---\n", sub)
writeLines('project:\n title: "test"\n', file.path(tf, "_quarto.yml"))
system(paste0("quarto inspect ", tf, "/main.qmd | grep project"))
system(paste0("quarto inspect ", tf, "/sub/sub.qmd | grep project"))
```
getting:
```
> system(paste0("quarto inspect ", tf, "/main.qmd | grep project"))
"project": "../../../private/tmp/RtmpAMjixD/file1842c7157d908"
> system(paste0("quarto inspect ", tf, "/sub/sub.qmd | grep project"))
"project": "../../../../private/tmp/RtmpAMjixD/file1842c7157d908"
```
In https://github.com/rstudio/rstudio/pull/11201#issuecomment-1128685959 I worked around it by by using `workingDir` but I was wondering if this was an issue.
```
% quarto --version
0.9.415
``` | {
"assignee": null,
"comments": 2,
"created_at": "2022-05-17T10:24:17Z",
"creator": "romainfrancois",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 906,
"state": "open",
"title": "`quarto inspect` and temporary directories",
"url": "https://github.com/quarto-dev/quarto-cli/issues/906"
} |
Quarto [shortcodes](https://quarto.org/docs/authoring/shortcodes.html) are a powerful, yet non-standard, extension to pandoc markdown syntax. Having them separated as reusabe lua filter, located at https://github.com/pandoc/lua-filters or in a separate git repository would allow to use this feature independently from Quarto and help to agree on common markdown extensions instead of every tool having its own extensions. The current implementation is [somwhere in the Quarto sources](https://github.com/quarto-dev/quarto-cli/blob/main/src/resources/filters/quarto-pre/shortcodes.lua). I managed to use it with a Quarto installation this way:
~~~bash
#!/bin/bash
export QUARTO_FILTER_PARAMS=$(echo '{"results-file":"tmp.html"}' | base64)
FILTER=/opt/quarto/share/filters/quarto-pre/quarto-pre.lua
INPUT='{{< pagebreak >}} {{< meta title >}}'
pandoc -L $FILTER <(echo "$INPUT") -M title=test
~~~
result:
~~~html
<p><div style="page-break-after: always;"></div> test</p>
~~~
This use is obviously fragile. I would welcome an official release of shortcodes as lua filter. I guess that it's enough to combine `shortcodes.lua` and `shortcodes-handlers.lua` and to provide an alternative to lua [function call param](https://github.com/quarto-dev/quarto-cli/blob/main/src/resources/filters/quarto-pre/shortcodes-handlers.lua#L68) to get the the list of custom shortcode files (could be a document meta variable or an environment variable such as `FILTER_SHORTCODES`). Sure I could just copy and adjust the code and add it to [lua-filters](https://github.com/pandoc/lua-filters) but then shortcodes feature is forked and with further evolution of Quarto we likely have two slightly differing sets and types of shortcodes.
**tl;dr:** it makes sense to reuse shortcodes independently from Quarto but this should be made easy and stable.
| {
"assignee": null,
"comments": 4,
"created_at": "2022-05-17T07:04:34Z",
"creator": "nichtich",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 904,
"state": "closed",
"title": "Factor out shortcodes as pandoc-filter",
"url": "https://github.com/quarto-dev/quarto-cli/issues/904"
} |
Hi, I've been trying to debug a YAML parsing error
`ERROR: YAMLError: can not read a block mapping entry; a multiline key may not be an implicit key at line 14, column 1:`
in my Quarto presentation, but I'm not sure how to go about doing this in a productive way --- I've just been removing stuff and checking to see if it's still broken, but it's not viable to keep doing that. Would you happen to have any tips on how to debug issues like these?
(The issue is probably not with the front matter.) | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-05-17T04:17:32Z",
"creator": "ym-han",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 903,
"state": "closed",
"title": "How to debug YAML parsing errors?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/903"
} |
## Problem description
I've created a new Quarto Book project under `~/tmp_quarto_book` via RStudio as [described here](https://quarto.org/docs/books/#rstudio).
While this renders fine via the Quarto CLI...
```sh
quarto render --to pdf
```
<details><summary>Output</summary>
```
[1/4] index.qmd
processing file: index.rmarkdown
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: index.knit.md
[2/4] intro.qmd
processing file: intro.rmarkdown
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: intro.knit.md
[3/4] summary.qmd
processing file: summary.rmarkdown
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: summary.knit.md
[4/4] references.qmd
pandoc
to: latex
output-file: index.tex
standalone: true
toc: true
number-sections: true
top-level-division: chapter
pdf-engine: xelatex
variables:
graphics: true
tables: true
default-image-extension: pdf
filters:
- crossref
- citeproc
metadata
crossref:
chapters: true
documentclass: scrreprt
papersize: letter
classoption:
- DIV=11
- numbers=noendperiod
header-includes:
- '\KOMAoption{captions}{tableheading}'
block-headings: true
bibliography:
- references.bib
editor: visual
title: tmp_quarto_book
author: Jane Doe
date: 5/16/2022
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
running xelatex - 2
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
Output created: _book/tmp_quarto_book.pdf
```
</details>
... an error message is shown when the rendering is performed via RStudio's <kbd>Render Book</kbd> button (to `PDF Format`):
<details><summary>Output</summary>
```
Rendering:
[1/4] index.qmd
processing file: index.rmarkdown
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: index.knit.md
[2/4] intro.qmd
processing file: intro.rmarkdown
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: intro.knit.md
[3/4] summary.qmd
processing file: summary.rmarkdown
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: summary.knit.md
[4/4] references.qmd
pandoc
to: latex
output-file: index.tex
standalone: true
toc: true
number-sections: true
top-level-division: chapter
pdf-engine: xelatex
variables:
graphics: true
tables: true
default-image-extension: pdf
filters:
- crossref
- citeproc
metadata
crossref:
chapters: true
documentclass: scrreprt
papersize: letter
classoption:
- DIV=11
- numbers=noendperiod
header-includes:
- '\KOMAoption{captions}{tableheading}'
block-headings: true
bibliography:
- references.bib
editor: visual
title: tmp_quarto_book
author: Jane Doe
date: 5/16/2022
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
running xelatex - 2
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
ERROR: InvalidData: stream did not contain valid UTF-8
```
</details>
I have no clue where the error **`InvalidData: stream did not contain valid UTF-8`** at the end stems from. The PDF seems to be built fine though.
## Setup
I use
- Ubuntu 22.04
- RStudio 2022.06.0-daily+406 "Spotted Wakerobin" Daily (5e9b6b93c1665966df7f5acca1cb9590f4e004e5, 2022-05-15) for Ubuntu Jammy
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
- Latest Quarto CLI installed from GitHub releases:
```sh
$ apt list --installed quarto
Listing... Done
quarto/now 0.9.414 amd64 [installed,local]
``` | {
"assignee": null,
"comments": 1,
"created_at": "2022-05-16T23:27:22Z",
"creator": "salim-b",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 902,
"state": "closed",
"title": "RStudio: `ERROR: InvalidData: stream did not contain valid UTF-8`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/902"
} |
How can I animate a bullet point inside a list in a Reactive.js animation?
This code generates an unwanted space between the last and previous bullet points:
```
- Bullet point
- Bullet point
::: {.fragment .fade-in}
::: {.fragment .highlight-red}
- Bullet point
:::
:::
```
Removing the space between the bullets does not help:
```
- Bullet point
- Bullet point
::: {.fragment .fade-in}
::: {.fragment .highlight-red}
- Bullet point
:::
:::
```
I suspect that there is a way to do this that I haven't been able to find. Since this is such a common scenario, it would be great if it was added to the Presentations/Revealjs documentation. | {
"assignee": null,
"comments": 3,
"created_at": "2022-05-16T18:45:27Z",
"creator": "mroavi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 901,
"state": "closed",
"title": "Revealjs: Fragment animation of a bullet point inside a list",
"url": "https://github.com/quarto-dev/quarto-cli/issues/901"
} |
See https://www.fharrell.com/post/rflow
A tab which contains a margin note will expand to take the whole page and render incorrectly. The margin note appears not to display sadly.
<img width="1840" alt="image" src="https://user-images.githubusercontent.com/261654/168650960-be2584a8-b64a-4e20-8f31-cfc93a910cbd.png">
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-05-16T17:38:14Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 900,
"state": "closed",
"title": "Margin Notes inside of tabset cause layout issues",
"url": "https://github.com/quarto-dev/quarto-cli/issues/900"
} |
Currently all Rmd or qmd files will be rendered when previewing site. There seems no option to ignore certain file (e.g., rmd child) or folder. It will be very useful to have such option. | {
"assignee": null,
"comments": 7,
"created_at": "2022-05-16T15:40:53Z",
"creator": "psychelzh",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 898,
"state": "closed",
"title": "Support ignore certain Rmd or qmd file for quarto website",
"url": "https://github.com/quarto-dev/quarto-cli/issues/898"
} |
I am wanting to use Quarto to create a book-based website and a PDF document from the same code. Using RStudio, I created a new Quarto Book project with the default files, which works and produces both a website and PDF from the same documents. However, when I start trying to include custom LaTeX code through the _quarto.yml file, I get an error.
The specific _quarto.yml file I am using alongside the default files included with the quarto project through RStudio is as follows:
```
project:
type: book
book:
title: "quarto-test-project"
author: "Jane Doe"
date: "5/16/2022"
chapters:
- index.qmd
- intro.qmd
- summary.qmd
- references.qmd
bibliography: references.bib
format:
html:
theme: cosmo
pdf:
include-in-header:
text: |
\usepackage{eplain}
\usepackage{easy-todo}
editor: visual
```
The only change to this file versus the original file is the include-in-header lines, which I took from the Quarto example on the website. This produces the following error:
```
Project _quarto.yml validation failed.
In file C:\Users\location\to\the\quarto-test-project\_quarto.yml
(line 20, column 5 through line 23, column 31) Key pdf has value include-in-header:
text: |
\usepackage{eplain}
\usepackage{easy-todo}, which must be 'default'
```
The expected outcome is that the project would run, producing the website and the PDF where the PDF has the designated text included in the header of the TeX file. I don't see anything in the documentation on the website that indicates that this is an invalid way to organize and use a Quarto project.
I am using:
- quarto version 0.9.193
- RStudio 2022.02.1+461 "Prairie Trillium" Release (8aaa5d470dd82d615130dbf663ace5c7992d48e3, 2022-03-17) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
- R version 4.1.3 (2022-03-10)
- Platform: x86_64-w64-mingw32/x64 (64-bit)
- Running under: Windows 10 x64 (build 19044) | {
"assignee": null,
"comments": 2,
"created_at": "2022-05-16T15:16:27Z",
"creator": "AnthonyRaborn",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 897,
"state": "closed",
"title": "Quarto yaml validation fails for include-in-header: text: for PDFs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/897"
} |
<details>
<summary>Minimal working example</summary>
```md
---
title: "Habits"
author: "John Doe"
format:
revealjs:
incremental: false
footer: "Footer text"
---
## Minimal working example
Normal alignment
- Element 1
- Element 2
* Element 3
:::: {.columns}
::: {.column width="50%"}
Buggy alignment
- Element 1
- Element 2
* Element 3
:::
::: {.column width="50%"}
Buggy alignment
- Element 1
- Element 2
* Element 3
:::
::::
```
</details>
produces
| {
"assignee": null,
"comments": 7,
"created_at": "2022-05-16T12:44:56Z",
"creator": "mroavi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 892,
"state": "closed",
"title": "Lists are not aligned properly inside `.columns` div containers with Revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/892"
} |
Hi,
as you can see below the footnote is above the text.
The code of that slide is
~~~
## CSV^[only a test] {.center}
```{.txt}
nome,note
"Marco,Bianchi","Lorem
Ipsum"
Ciccio Bombo,Lorem
"Bianca ""Stella"" Balti",Ipsum
```
- [csvkit](https://csvkit.readthedocs.io/)
- 💘 [Miller](https://miller.readthedocs.io/en/latest/)
- 💘 [VisiData](https://ondata.github.io/guidaVisiData/)
~~~
My settings are
```
title: "My title"
#subtitle: ""
format:
revealjs:
slide-number: true
preview-links: auto
auto-stretch: false
navigation-mode: vertical
center-title-slide: false
lang: it
hash-type: number
self-contained: false
resources:
- demo.pdf
```
Thank you
| {
"assignee": null,
"comments": 2,
"created_at": "2022-05-16T06:45:56Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 890,
"state": "closed",
"title": "reveal presentation: footnotes in wrong position, using vertical slides",
"url": "https://github.com/quarto-dev/quarto-cli/issues/890"
} |
Along the lines of #859 I tried the following in a Book project:
```yaml
format:
html:
header-includes: |
<link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.1.1/css/all.min.css"
rel="stylesheet"/>
self-contained: true
```
Sadly, when I preview the web site, the link is never inserted (and the icon won't render).
If I turn off `self-contained` the icons are visible, but my other diagrams produced by a filter are then broken. Is it possible to have `self-contained` and `head-includes` working together? | {
"assignee": null,
"comments": 5,
"created_at": "2022-05-15T19:42:11Z",
"creator": "fuhrmanator",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 889,
"state": "closed",
"title": "Font awesome won't load for me in the HTML of a book (self-contained: true)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/889"
} |
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