page_content
stringlengths 0
46.9k
| metadata
dict |
|---|---|
### Bug description
I'm trying to include a code block in a numbered list and I'm getting unexpected output:
Input:
````md
---
title: "Test"
author: "Andew Barros"
format: html
---
1. Question
```{r}
1 + 1
```
1. Question 2
````
Output:
```
1. Question
1 + 1
::: {.cell-output .cell-output-stdout} [1] 2 ::: :::
2. Question 2
```
(The line with ::: is visible in the output both when rendered to html and PDF).
If I render that same file through the rmarkdown pathway -- I get the intended output
I'm using RStudio 2022.07.2 Build 576 on MacOS 13.0.1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-11-14T19:42:03Z",
"creator": "ajb5d",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3325,
"state": "open",
"title": "Add lint warning when code block is indented inconsistently inside list",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3325"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3322
<div type='discussions-op-text'>
<sup>Originally posted by **AlbertRapp** November 14, 2022</sup>
Would it be possible to transform the `.remark` class into a `#rem-` name such that remarks are numbered and become cross-referenceable?
According to the [docs](https://quarto.org/docs/authoring/cross-references.html#theorems-and-proofs) this is intended behavior.
In mathematics, we use remarks all the time and cross-reference them too. That's easy in LaTeX. Would be great if that's possible in Quarto too.</div> | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-11-14T18:46:37Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3323,
"state": "open",
"title": "Numbered and cross-referencable Remarks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3323"
} |
To reproduce:
1. Create a minimal diagram on diagrams.net. (I created a box with the text "TEST" inside)
2. Export as SVG (using defaults)
3. Include SVG file as image in quarto pptx presentation and render to pptx
4. Open in PowerPoint (Microsoft 365 version 2202)
5. Get blank image with this notice:
I do not have access to Trust Center settings as per this Stack Overflow answer: https://stackoverflow.com/a/22183081
Dropping the file in to a PowerPoint file directly (i.e. bypassing quarto) works fine. | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-14T14:37:59Z",
"creator": "ropeladder",
"is_pull_request": false,
"labels": [
"needs-repro",
"third-party"
],
"locked": false,
"milestone": null,
"number": 3315,
"state": "closed",
"title": "PowerPoint blocks included SVG images from diagrams.net",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3315"
} |
### Bug description
Hi. I'm trying to render a table within a r-code chunk with `knitr::kable()` in a two column setting, but got the following trouble in the background jobs tab:
```
compilation failed- error
Package longtable Error: longtable not in 1-column mode.
See the longtable package documentation for explanation.
Type H <return> for immediate help.
...
l.324 \begin{longtable}
[]{@{}rrr@{}}
```
As said, I've been required a two column setting (journal style), so my YAML header and a minimal code is something like
````
---
format: pdf
classoption: twocolumn
---
# Enough to get the error
```{r}
knitr::kable(mtcars)
```
````
Running RStudio 2022.07.1 Build 554 on Linux Mint 20.3
I hope this help out to improve Quarto's functionality and use cases, since the two column setting is very much required when working on an academic settings.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2022-11-14T14:31:54Z",
"creator": "emilianomm",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3314,
"state": "closed",
"title": "`compilation failed -error` upon rendering a table with knitr::kable()",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3314"
} |
### Bug description
Hello,
I am trying to embed a youtube video into a Quarto document (v1.2.269 on windows 11 pro).
However, I noticed that the video embedding failed when setting either `embed-resources: true` or `self-contained: true` in the YAML.
The same occurred using the `{{< video LINK >}}` shortcode or `iframe`. `iframe` works only after setting `data-external="1"`; e.g. `<iframe data-external="1" src="LINK"></iframe>`
****
The following example does not work
```
---
title: "Quarto"
format:
html:
toc: true
self-contained: true
---
{{< video https://www.youtube.com/embed/wo9vZccmqwc >}}
```
```
---
title: "Quarto"
format:
html:
toc: true
embed-resources: true
---
{{< video https://www.youtube.com/embed/wo9vZccmqwc >}}
```
****
While this works:
```
---
title: "Quarto"
format:
html:
toc: true
---
{{< video https://www.youtube.com/embed/wo9vZccmqwc >}}
```
****
Is this an expected behaviour?
Thanks, Ahmed
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-11-14T12:32:34Z",
"creator": "elgabbas",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3310,
"state": "closed",
"title": "embedding video failed when using `embed-resources: true` or `self-contained: true` in the YAML.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3310"
} |
### Bug description
html option `number-sections: false` does not remove numbering in
html `<head><title>` metadata, leaving numbering in tabs.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-12T19:20:40Z",
"creator": "alxsimon",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3304,
"state": "closed",
"title": "html `number-sections: false` does not remove numbering from html <head>",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3304"
} |
### Bug description
Hello,
I am trying to run a bash code chunk using Quarto (`v1.2.269`). The following works nicely
````
---
format:
html:
kernel: knitr
---
```{r}
```
```{bash}
echo "AA"
```
````
However, it uses the default git bash software, which does not support all bash/shell commands. I would like to use Ubuntu [Windows Subsystem for Linux (WSL)] installation instead [on windows 11 pro 22H2].
I was able to change the terminal in Rstudio [`v2022.07.2+576.`] as shown in the next screenshot. It works but only while using the terminal tab.
However, this does not apply to code chunks. I tried to change (force) Quarto to use a specific version of bash using the `engine.path` and `engine.opts` arguments without success [the same also occurred in VS code].
````
```{bash engine.path="C:/WINDOWS/system32/wsl.exe", engine.opts="-d Ubuntu-20.04"}
echo "Some text"
```
````
I receive the following error:
> running: C:/WINDOWS/system32/wsl.exe -d Ubuntu-20.04 -c "echo \"Some text\""
Quitting from lines 20-21 (211.qmd)
>Error in engine(options) : I
> Calls: .main ... call_block -> block_exec -> in_input_dir -> in_dir -> engine
In addition: Warning message:
In system2(cmd, code, stdout = TRUE, stderr = TRUE, env = options$engine.env) :
> running command '"C:/WINDOWS/system32/wsl.exe" -d Ubuntu-20.04 -c "echo \"Some text\""' had status 65535
Execution halted
Note that running the following command in the command prompt `"C:/WINDOWS/system32/wsl.exe" -d Ubuntu-20.04 echo "Some text"` works with printing the 'some text' string. I am not an expert in this, but I think there may be a problem with additional quotations and the `-c` argument.
Could you please help me with using the wsl installation of Ubunto in Quarto?
> This may be related to this issue posted on [RStudio](https://github.com/rstudio/rstudio/issues/7493).
Thanks, Ahmed
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 3,
"created_at": "2022-11-12T14:02:56Z",
"creator": "elgabbas",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"windows"
],
"locked": false,
"milestone": null,
"number": 3302,
"state": "closed",
"title": "Running bash chunks using wsl",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3302"
} |
Hi,
I am not sure if this is a bug or a feature, although but I have not been able to find it documented nor in other bugs reports.
I have Quarto document with output format `revealjs`. I include in my code chunks the options `echo: true` and `output-location: column` (the same happens with `column-fragment`).
It works as expected when in a regular slide. But if the code chunk in under panel tabset the output is not shown in an adjacent column, but below the code. Here is an example
````
---
title: "test"
format: revealjs
---
## Works as expected
Code in the left and `4` shown in an adjacent column.
```{r}
#| echo: true
#| output-location: column
2 + 2
```
## Tabset
::: {.panel-tabset}
### Tab 1
First tab
### Tab 2
Here output `4` is shown below the code
```{r}
#| echo: true
#| output-location: column
2 + 2
```
:::
````
Not sure if relevant in this case, but for completeness, I am using RStudio 2022.07.02 (build 576) with `knitr` engine under Linux (Lubuntu 22.10).
Thanks a lot in advance! | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-12T11:38:22Z",
"creator": "albarran",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3301,
"state": "open",
"title": "output-location: column does not work with tabsets",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3301"
} |
### Bug description
When I render a qmd file to a website, the index.html points to the incorrect file. reproducible exampl here: https://github.com/poldrack/talks-nipreps. inside cloned repo:
```
rm -rf docs
quarto render NiPreps.qmd
```
This renders to docs/talk - index.html in that folder should redirect to NiPreps.html, but instead redirects to LICENSE.html:
```
% more docs/talk/index.html
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>Redirect to LICENSE.html</title>
<meta http-equiv="refresh" content="0;URL='LICENSE.html'" />
</head>
<body>
</body>
</html>
```
This is using quarto CLI version 1.2.267 on Mac OS 12.6
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-11-11T19:16:11Z",
"creator": "poldrack",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3297,
"state": "closed",
"title": "index.html redirects to incorrect file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3297"
} |
In the case of
```
listing:
contents:
- should be first.qmd
- I'm second.qmd
- third.qmd
```
the default ordering of listing items will be based on title, which in the case above, would list articles as:
1. I'm second
2. should be first
3. third
Using `sort` with its current implementation, I can only sort by a listing field within each document, which may not be appropriate for organizing the listings on the page. I would like the ability to sort the listing order based on the order the items are specified in `contents`
My workaround is to create a yml file with the listing contents in the order I desire, but I'd rather not add additional complexity
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-11-11T18:22:18Z",
"creator": "kmasiello",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3296,
"state": "closed",
"title": "Feature request - sort listings by specified order",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3296"
} |
### Bug description
Cross references to a figure I create in a Jupyter Notebook cell do not render in other cells in the notebook.
I've tested this on both Windows 11 and Ubuntu 22.10. Quarto version `1.2.269`.
How to reproduce:
Create a test notebook with a raw cell, a code cell and a markdown cell.
```
---
title: Test
format:
html:
code-fold: true
jupyter: python3
---
```
```
#| label: demolabel
#| fig-cap: Figure caption
import matplotlib.pyplot as plt
fig, ax = plt.subplots()
ax.plot([1, 2, 3])
```
```
See @demolabel
```
Here's the result when I use `quarto preview test.ipynb`. As you can see @demolabel hasn't been turned into a cross reference to the figure, which is what I expected.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-11T17:45:46Z",
"creator": "jensodeg",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3295,
"state": "closed",
"title": "Computed notebook figure cross reference not rendered in html format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3295"
} |
### Bug description
My apologies if i put this on the wrong page, or if it should be a feature request. I have not been able to find documentation for aligning mermaid diagrams.
Mermaid diagrams appear to be left-aligned for html and docx outputs. I can't change this with `fig-align: center` in the yml file, nor with `%%| fig-align: center` in the mermaid code.
For pdf, `fig-align` appears to work as intended in the yml, but not in the mermaid code.
````
project:
type: book
book:
title: "Mermaid alignment"
chapters:
- index.qmd
format:
html:
theme: cosmo
fig-align: center
docx:
fig-align: center
# pdf:
# documentclass: scrreprt
# fig-align: right
editor: source
````
````
```{mermaid}
%%| fig-cap: Mermaid diagram
%%| fig-align: center
flowchart TB
a --> b
b --> c
```
````
Versions
- quarto version 1.2.269
- R version 4.2.2 (2022-10-31 ucrt)
- Platform: x86_64-w64-mingw32/x64 (64-bit)
- RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) 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
Output
html:
docx:
pdf (when not commented out):
repo
https://github.com/VMTdeJong/Quarto-mermaid-align
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-11-11T13:51:29Z",
"creator": "VMTdeJong",
"is_pull_request": false,
"labels": [
"bug",
"mermaid"
],
"locked": false,
"milestone": "v1.3",
"number": 3294,
"state": "closed",
"title": "Alignment of mermaid diagrams",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3294"
} |
### Bug description
column-margin contents have arbitrary and broken placement if used within panel-tabset
Probably related to closed [issue](https://github.com/quarto-dev/quarto-cli/issues/2341 )
Anecdotally, margin height seems to be set relative to the tab's contents, and then moved lower, and lower, until it trails off onto content below. In my use case I have tabsets stacked down a page and so margin contents end up escaping one tabset and overlapping another lower one, especially with contents that are different sized images. Reproduced on both chrome and Firefox, but have seen intermittent correct alignment on Firefox that then breaks when moving through toc links.
```
---
title: "column-margin Misplacement in panel-tabset Reproducible Example"
format:
html
---
# Header 1
::: {.panel-tabset}
### Subheader 1
::: {.column-margin}
Margin Text 1
:::
<!--  -->
### Subheader 2
::: {.column-margin}
Margin Text 2
:::
:::
```
Happened with latest stable build and currently with nightly
quarto -v
99.9.9
`
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2 fastmap_1.1.0 cli_3.4.1 htmltools_0.5.3 tools_4.2.2 rstudioapi_0.14 yaml_2.3.6 rmarkdown_2.17 knitr_1.40 xfun_0.34 digest_0.6.30 rlang_1.0.6 evaluate_0.17
`
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-11-10T21:27:16Z",
"creator": "rexdouglass",
"is_pull_request": false,
"labels": [
"bug",
"articles"
],
"locked": false,
"milestone": "v1.3",
"number": 3280,
"state": "closed",
"title": "column-margin Misplacement in panel-tabset",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3280"
} |
### Bug description
I have the below code in a Quarto project and I'm trying to render to pdf.
````{r}
#| label: fig-ash-map
#| fig-cap: "Map of Town of Ashland"
ashland <- st_read('https://services2.arcgis.com/sKZWgJlU6SekCzQV/arcgis/rest/services/Ashland_Boundary/FeatureServer/0/query?outFields=*&where=1%3D1&f=geojson', quiet = TRUE)
leaflet(ashland) %>%
addTiles() %>%
addPolygons()
````
I get the following error that was not occurring previously:
> Error: Functions that produce HTML output found in document targeting pdf output.Please change
> the output type of this document to HTML. Alternatively, you can allow
> HTML output in non-HTML formats by adding this option to the YAML front-matter ofyour quarto file:
>
> prefer-html: true
>
> Note however that the HTML output will not be visible in non-HTML formats.
I've updated quarto cli to the 1.2.269 Candidate Release on Windows 11 Pro. It worked fine on my other machine and all packages are updated. My yml includes the following settings for pdf export:
> knitr:
> opts_chunk:
> echo: false
> warning: false
> message: false
>
> format:
> html:
> theme: lumen
> pdf:
> documentclass: scrreprt
Please help! I was having no issue with Quarto exporting these out to a pdf previously but am now all of a sudden.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 8,
"created_at": "2022-11-10T20:44:03Z",
"creator": "ericvmai",
"is_pull_request": false,
"labels": [
"bug",
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3279,
"state": "open",
"title": "error with pdf output and html function (leaflet)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3279"
} |
### Bug description
## Description
This is only happening on my Apple M1 (Big Sur). Works fine on RStudio Cloud. I am using Quarto version 1.2.269. Clean install of most recent R.
When a child Rmd with a `gt()` call is in a subdirectory **and** a file with the same name is **not** in root, then Quarto render to html or Word fails with a "file cannot be opened" error.
* Does not happen with output to pdf.
* Only happens if child is in a subdirectory.
* Only happens if a file with the same name is not in root. So if `figures/child_indir.Rmd` was renamed to `figures/child.Rmd`, it works
* Does not happen if the `gt()` call is commented out. Seems very `gt()` and Mac specific.
* That the child is Rmd instead of qmd doesn't matter; same behavior if file ending changed to qmd.
* Works on RStudio Cloud (R 4.2.1) with both Quarto version 1.1.251 and version 1.2.269
* Clean install of R 4.2.2 and only packages need for this minimal example installed.
* Doesn't matter how I render via RStudio or `quarto render test.qmd` from terminal
* Does not happen if I change test.qmd to test.Rmd and use `rmarkdown::render("test.Rmd")`. Seems `quarto render` specific.
Quarto version v1.2.269 pre-release
## Reproducible example
File structure:
test.qmd
child.Rmd
figures/child_indir.Rmd
test.qmd
<pre>
---
format: html
---
# Works
```{r}
gt::gt(head(mtcars))
```
# This is what causes the error
```{r child="figures/child_indir.Rmd"}
```
# Works
```{r child="child.Rmd"}
```
</pre>
child.Rmd and figures/child_indir.Rmd. **These must have different names!** Below is all that is in the file. The `gt()` is the problem. Commenting that out or replacing with any other code (e.g. `flextable()`) causes the problem to go away.
<pre>
```{r}
gt::gt(head(mtcars))
```
</pre>
Error output is
<pre>
Quitting from lines 2-3 (/Users/eli.holmes/Desktop/deleteme3/figures/child_indir.Rmd)
Quitting from lines NA-3 (/Users/eli.holmes/Desktop/deleteme3/figures/child_indir.Rmd)
Error in readLines(con, warn = FALSE) : cannot open the connection
Calls: .main ... <Anonymous> -> enumerate_output_formats -> read_utf8 -> readLines
</pre>
## Expected result
The html or Word file should be produced.
## Session info
<pre>
> sessionInfo()
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.2
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] pillar_1.8.1 compiler_4.2.2 bslib_0.4.1
[4] jquerylib_0.1.4 tools_4.2.2 digest_0.6.30
[7] jsonlite_1.8.3 evaluate_0.18 lifecycle_1.0.3
[10] tibble_3.1.8 gtable_0.3.1 pkgconfig_2.0.3
[13] rlang_1.0.6 cli_3.4.1 yaml_2.3.6
[16] xfun_0.34 fastmap_1.1.0 withr_2.5.0
[19] dplyr_1.0.10 stringr_1.4.1 knitr_1.40
[22] generics_0.1.3 vctrs_0.5.0 sass_0.4.2
[25] grid_4.2.2 tidyselect_1.2.0 glue_1.6.2
[28] R6_2.5.1 fansi_1.0.3 rmarkdown_2.18
[31] ggplot2_3.4.0 magrittr_2.0.3 scales_1.2.1
[34] htmltools_0.5.3 gt_0.7.0 colorspace_2.0-3
[37] utf8_1.2.2 stringi_1.7.8 munsell_0.5.0
[40] cachem_1.0.6
</pre>
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-11-10T17:25:27Z",
"creator": "eeholmes",
"is_pull_request": false,
"labels": [
"bug",
"tables"
],
"locked": false,
"milestone": null,
"number": 3274,
"state": "closed",
"title": "Quarto render throws 'file not found' error with child Rmd/qmd with gt()",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3274"
} |
### Bug description
Thanks for all your work on this!
`output-location` should work when placed in the YAML header. Currently this option only works when placed inside individual chunk options. Example:
````md
---
format: revealjs
knitr:
opts_chunk:
echo: true
output-location: fragment
---
```{r}
5 + 5
```
````
Tested on Fedora 37 and Windows 10, and development version and on 1.1.251.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-11-09T22:02:40Z",
"creator": "wklimowicz",
"is_pull_request": false,
"labels": [
"bug",
"documentation",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 3261,
"state": "closed",
"title": "`output-location` doesn't work in YAML header",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3261"
} |
Quarto Version: 1.2.246
flextable 0.8.3 (latest)
### Bug description
When I render (in RStudio or terminal), it hangs if I have a flextable. Hanging started with Quarto 1.2 release. Still works fine with Quarto 1.1 on RStudio Cloud.
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
```
---
format: docx
---
```{r}
flextable::flextable(head(mtcars))
```
```
The output is this and then after the last line, the render spinwheel spins forever.
```
processing file: test.qmd
|.............. | 20%
ordinary text without R code
|............................ | 40%
label: unnamed-chunk-1 (with options)
List of 2
$ results: chr "asis"
$ eval : logi FALSE
|.......................................... | 60%
ordinary text without R code
|........................................................ | 80%
label: unnamed-chunk-2
|......................................................................| 100%
ordinary text without R code
output file: test.knit.md
pandoc
to: docx
output-file: test.docx
default-image-extension: png
metadata
editor: visual
```
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
-
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
2022.07.1 Build 554
But same rendering hang happens when I do `quarto render test.qmd`
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
Apple M1, BigSur
**Note renders fine on RStudio Cloud with Quarto 1.1.251** | {
"assignee": null,
"comments": 3,
"created_at": "2022-11-09T21:19:48Z",
"creator": "eeholmes",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3257,
"state": "closed",
"title": "Rendering to docx hangs when flextable used; new issue with Quarto v 1.2",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3257"
} |
### Bug description
There seems to be an issue with plotly inside of divs that normally shouldn't be run and displayed e.g. in the following qmd file:
````md
---
title: "Untitled"
# prefer-html: true
format:
html: default
pdf: default
---
# Test
::: {.content-hidden when-format="html"}
Will not appear in HTML.
:::
This works:
::: {.content-hidden unless-format="html"}
Should appear in the html
```{r}
knitr::kable(mtcars, format = "html")
```
:::
The following fails with
> Error: Functions that produce HTML output found in document targeting pdf output.
::: {.content-hidden unless-format="html"}
Should appear in the html, but not in the pdf:
```{r}
library(tidyverse)
plt <- ggplot(mtcars, aes(mpg, disp)) +
geom_point()
plotly::ggplotly(plt)
```
:::
or when forced through `prefer-html: true` with:
> LaTeX Error: Missing \begin{document}.
>
> See the LaTeX manual or LaTeX Companion for explanation.
> Type H <return> for immediate help.
> ...
>
> l.78 <
> script src="test_files/libs/htmlwidgets-1.5.4/htmlwidgets.js"></script>
````
quarto version: 1.2.269
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-11-09T15:16:46Z",
"creator": "jmbuhr",
"is_pull_request": false,
"labels": [
"documentation",
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3254,
"state": "open",
"title": "`::: {.content-hidden unless-format=\"html\"}` with `plotly` seems to end up in pdf output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3254"
} |
### Bug description
When I use the command 'quarto publish' every post/page is recreated/updated in html, regardless of whether the page/content changed or not.
- Is this the correct/expected behavior?
using the above method, dates on the sitemap are not reflecting when the content was most changed
- how do you publish updates to some pages but not all pages (i.e. so the sitemap and dates are correct)?
another scenerio is you might change or remove a category on one page, quarto publish would regenerate every since post page and the sitemap. the underlying content technically didn't change on the pages, only meta-data displayed in one page
- why does this scenario record that the page/post content change for every page?
it seems that sitemap updated dates should relate to content, not navigation/meta-data ?
Thanks
Tom
vscode+extension
windows 11
github/actions
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-11-08T21:47:45Z",
"creator": "thomashallam",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3251,
"state": "closed",
"title": "sitemap.xml generation incorrect date?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3251"
} |
### Bug description
A markdown cell in a .ipynb that contains a number will be printed in a very funky way using the weasyprint engine and the format is PDF
Using the following code as a markdown cell in a ipynb
```
one string 212 another string
```
The generated pdf will look like this
| {
"assignee": null,
"comments": 0,
"created_at": "2022-11-08T19:23:53Z",
"creator": "a0th",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3248,
"state": "open",
"title": "Issue with weasyprint and markdown numbers in PDF reports",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3248"
} |
### Bug description
I'm not sure whether that's a {gt} or a Quarto problem. Since the {gt} code itself runs, I put it here.
Using IDs in {gt} tables causes issues with rendering a Quarto document. I don't know what the error means so I'll just put it here.
```
Error running filter /opt/quarto/share/filters/quarto-pre/quarto-pre.lua:
/opt/quarto/share/filters/quarto-pre/quarto-pre.lua:2555: attempt to concatenate a nil value (local 'v')
stack traceback:
/opt/quarto/share/filters/quarto-pre/quarto-pre.lua:2562: in function </opt/quarto/share/filters/quarto-pre/quarto-pre.lua:2560>
```
The code that caused this error was (that's also the whole file)
```
ggplot2::mpg |>
gt::gt(id = 'myTbl')
```
## Version info
RStudio: 2022.07.2 Build 576
OS: Ubuntu 20.04.5 LTS
Quarto: 1.2.267
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-11-08T19:20:31Z",
"creator": "AlbertRapp",
"is_pull_request": false,
"labels": [
"bug",
"duplicate",
"tables"
],
"locked": false,
"milestone": null,
"number": 3247,
"state": "closed",
"title": "Quarto does not render with some {gt} table IDs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3247"
} |
### Bug description
So I have some issues with including pictures in a quarto project, and it seems to be persisent even in very simple examples, so I think it's a bug. As this is concerned with folder structure, the issue is a bit hard to reproduce. Bear with me, and please ask and I'll happy to clarify.
Let's start with something that does work:
I have a project structure like this:
```
.
├── img
│
└── test.png
├── index.qmd
├── _quarto.yml
└── test.qmd
```
e.g. a yaml, a directory called img with an image 'test.png', an index.qmd
the yaml contains this:
```
project:
type: book
book:
title: "this is a title"
chapters:
- index.qmd
```
the index.qmd contains this (I put forward brackes on the backticks to not mess with the formatting in here, but in the file the forward slashes are of course not present)
```
this works
\```{r}
library(knitr)
include_graphics('img/test.png')
\```
```
ok, so this works. test.qmd in the qmd-directory contains the the same content as index.qmd.
However, suppose I want to keep my qmd-files in a subdirectory, and have the img folder in the project dir. That would look Like this:
```
.
├── img
│
└── test.png
├── index.qmd
├── qmd
│
└── test.qmd
└── _quarto.yml
```
the yaml now looks like this, as I include a subfolder called 'qmd' with quarto files.
```
project:
type: book
book:
title: "this is a title"
chapters:
- index.qmd
- qmd/test.qmd
```
index.qmd have the same content as before. test.qmd in the qmd-directory contains the the same content as index.
When I run quarto preview, the image is displayed in the index.qmd file. However, the file test.qmd gives cause to the following error
```
Error in include_graphics("img/test.png") :
Cannot find the file(s): "img/test.png"
```
I cannot seem to get around this. including this in the yaml:
```
output-dir: _output
execute-dir: project
```
does not work. Neither does Setting this in the chunk:
```
knitr::opts_chunk$set(root.dir = normalizePath("img"))
knitr::opts_chunk$get("root.dir")
```
I also tried making an _eviroment file in the root dir with the following content:
```
QUARTO_PROJECT_DIR='path-to-project-dir'
```
still no dice.
the strange thing about it is that non-image related inputs, like using read.csv() works fine (e.g. putting a csv file in the img folder and loading that works. it's only related to images, as fas as I can tell, where the project dir fails.)
this also applies to markdown style images . It tries to find the folder under 'qmd' no matter how I try to change it (also: putting the img-folder under the 'qmd' folder also fails, which you would think it wouldn't.
I updated to version 1.2.237 of quarto to see if using the project envir variables would work. I'm on Manjaro linux w. i3, fully updated.
I use the cli version of quarto, not thru Rstudio.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.b | {
"assignee": "cderv",
"comments": 11,
"created_at": "2022-11-08T16:45:23Z",
"creator": "emilBeBri",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"file-systems",
"stale"
],
"locked": false,
"milestone": "v1.4",
"number": 3245,
"state": "open",
"title": "putting qmd-files in a subdir causes image-rendition to fail, wether it's markdown style or with knitr::include_graphics()",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3245"
} |
### Bug description
Hi all,
I am trying to write a presentation using Reveal.js that mix R and python code. I think it is possible to mix code in Quarto documents, I do not understand what's going on here.
It seems not possible, or I am missing something. Here is a simple example of qmd file that does not compile.
````md
---
title: "test"
format: revealjs
---
```{r}
#| echo: true
hist(rnorm(1000))
```
---
```{python}
#| echo: true
import matplotlib.pyplot as plt
plt.plot([1, 2, 3, 4])
plt.ylabel('some numbers')
plt.show()
```
````
which gives an error concerning TCL:
> Error in py_call_impl(callable, dots$args, dots$keywords) :
_tkinter.TclError: Can't find a usable init.tcl in the following directories: [...]
I'm using the latest Quarto (1.2.267), under Windows 10 and RStudio 2022.07.1 Build 554. The python environment is created with only the latest versions of jupyterlab and matplotlib.
Thanks for you time !
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 7,
"created_at": "2022-11-08T15:32:15Z",
"creator": "NRaillard",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3244,
"state": "closed",
"title": "Mix R and python code in Quarto presentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3244"
} |
### Bug description
The number of the section is duplicated both in the table of contents and in the body.
Tested pdf engines: wkhtmltopdf, weasyprint, paged.js.
The following ipynb file
```
---
format: pdf
pdf-engine: wkhtmltopdf
number-sections: true
---
# H1
## H2
```
Will produce this PDF file
Quarto version: 1.1.251
Ubuntu 22.10
| {
"assignee": null,
"comments": 2,
"created_at": "2022-11-08T15:07:47Z",
"creator": "a0th",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3243,
"state": "open",
"title": "Duplicated number section when not using latex in PDF from ipynb",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3243"
} |
### Bug description
I am trying to edit the title slide layout for revealjs output using the title-slide.html partial. However, quarto complains that only title-block.html is acceptable. This is not the behavior that the [guide](https://quarto.org/docs/journals/templates.html#revealjs-partials) describes.
This example ends up in the error message:
```
---
title: "Title"
subtitle: "Subtitle"
author: "Author"
format:
revealjs:
template-partials:
- title-slide.html
---
## A minimal working example
::: {.callout-note }
## An MWE
- should be fully functional
- should be minimal
:::
```
The error says
```
ERROR: The format 'revealjs' only supports the following partials:
metadata.html
title-block.html
toc.html
Please provide one or more of these partials.
Error: The format 'revealjs' only supports the following partials:
metadata.html
title-block.html
toc.html
Please provide one or more of these partials.
at runPandoc (file:///Applications/quarto/bin/quarto.js:66010:31)
at async renderPandoc (file:///Applications/quarto/bin/quarto.js:66526:26)
at async Object.onRender (file:///Applications/quarto/bin/quarto.js:77072:32)
at async renderFiles (file:///Applications/quarto/bin/quarto.js:76455:21)
at async render (file:///Applications/quarto/bin/quarto.js:76781:20)
at async renderForPreview (file:///Applications/quarto/bin/quarto.js:87446:26)
at async render1 (file:///Applications/quarto/bin/quarto.js:87338:20)
at async preview (file:///Applications/quarto/bin/quarto.js:87344:20)
at async Command.fn (file:///Applications/quarto/bin/quarto.js:88492:9)
at async Command.execute (file:///Applications/quarto/bin/quarto.js:2739:13)
```
I am running quarto from the command line (`quarto preview file.qmd`) on macOS12.6.1.
If I provide `title-block.html`, there is no error message. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-08T13:40:14Z",
"creator": "mtthsdzwn",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3240,
"state": "closed",
"title": "revealjs partials: title-slide.html not accepted.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3240"
} |
### Bug description
The following minimal working example
``````
---
title: "MWE"
---
```{mermaid}
%%| label: fig-percentage
%%| fig-cap: Flowchart
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
```
```{mermaid}
//| label: fig-slash
//| fig-cap: Flowchart
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
```
``````
produces
The build/render log is
```
pandoc
to: html
output-file: mermaid.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: MWE
Output created: mermaid.html
```
Would be great to give a warning regarding the wrong code block metadata. For example:
```
Warning at line 17: mermaid code block uses %%| instead of //|
Warning at line 18: mermaid code block uses %%| instead of //|
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-11-08T04:35:54Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3235,
"state": "open",
"title": "Improve validation of mermaid code block",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3235"
} |
### Bug description
Originally reported at https://github.com/quarto-dev/quarto-cli/discussions/3218
Quarto supports [cross reference to book chapters](https://quarto.org/docs/books/book-crossrefs.html) but does **not** support to book parts.
[Minimal working example](https://github.com/quarto-dev/quarto-cli/files/9957180/3218.zip).
`quarto check` output
```
[✓] Checking Quarto installation......OK
Version: 1.2.117
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.9.10 (Conda)
Path: /home/raniere/mambaforge/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
[✓] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/raniere/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.16
[✓] Checking Knitr engine render......OK
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-11-08T02:44:09Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug",
"duplicate",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3234,
"state": "closed",
"title": "Support cross reference to book part",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3234"
} |
Not everyone knows either of these and the upwards arrow can easily render funny as well. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-11-08T00:50:44Z",
"creator": "kendonB",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4501,
"state": "open",
"title": "Change '^' to 'Ctrl' and the upwards arrow to 'Shift' ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4501"
} |
### Bug description
I am using Ubuntu 20.04 and am experiencing this issue in version 1.1.251 and 1.2.262 of quarto-cli. No editor/IDE was used, just terminal.
The minimal example in my case is one of the tutorial commands here: https://quarto.org/docs/books/
```
quarto create-project mybook --type book
```
With no other changes, if I open the book by running:
```
quarto preview mybook
```
The book works perfectly fine and the search bar functions as expected:
- If I search for something that isn't in the book, I see a *No results* result
- If I search for something that is in the book, I see several matches drop down
But if I open the book by running:
```
quarto render mybook
```
Followed by either:
```
firefox mybook/_book/index.html
```
or
```
microsoft-edge mybook/_book/index.html
```
I see the html book exactly as it was in the preview, all the links and formatting work fine, but the search bar does not work. No results (not even the phrase *No results*) pop up from the search bar regardless of what I type or enter. Is this expected behaviour when not using the preview command?
Thanks for any assistance.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-07T22:22:55Z",
"creator": "pvelayudhan",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3230,
"state": "closed",
"title": "Search works in HTML book preview, but not in rendered HTML book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3230"
} |
This will work around different versions of vs code using slightly different paths. | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-07T21:06:41Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"open-pr"
],
"locked": false,
"milestone": "v1.2",
"number": 3227,
"state": "closed",
"title": "preview: Don't prefix paths with `/` in case they already have that",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3227"
} |
### Bug description
Hi all,
I am trying to make some basic adjustments to a few files, and I wanted to set up the development version of the Quarto CLI.
* I `git clone`d a fresh version from my fork of `main`
* I then ran `configure.cmd` as direct and it doesn't complete successfully.
I think it has something to do with the `package/src/store_win_configuration.bat` file, in that it's not parsing the paths correctly. However, I'm not an experienced Windows shell developer, so I am not comfortable trying to fix it.
Can anyone help me out? I've included the output of the `configure.cmd` terminal output below. If it helps, I'm running on Windows 11 (dun dun dun).
```console
C:\Users\Jonathan Graves\Documents\GitHub\quarto-cli>configure.cmd
The system cannot find the path specified.
The system cannot find the file Graves\Documents\GitHub\quarto-cli\package\src\\..\..\configuration.
"Translated/recorded configuration settings from unix configuration script"
'win_configuration.bat' is not recognized as an internal or external command,
operable program or batch file.
The syntax of the command is incorrect.
A subdirectory or file \tools already exists.
Bootstrapping Deno...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
curl: (22) The requested URL returned error: 404
tar: Error opening archive: Failed to open 'deno-x86_64-pc-windows-msvc.zip'
Could Not Find C:\tools\deno-x86_64-pc-windows-msvc.zip
.
The system cannot find the path specified.
Configuring Quarto from C:\Users\Jonathan Graves\Documents\GitHub\quarto-cli
'quarto-bld.cmd' is not recognized as an internal or external command,
operable program or batch file.
Configuration done
Revendoring quarto dependencies
Downloading Deno Stdlib
The system cannot find the path specified.
NOTE: To use quarto please use quarto-cmd (located in this folder) or add the following path to your PATH
ECHO is off.
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-11-07T20:29:19Z",
"creator": "jlgraves-ubc",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "Future",
"number": 3225,
"state": "open",
"title": "Configure.cmd does not work when spaces are in path",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3225"
} |
### Bug description
Long strings in backticks or code chunks do not wrap - this can lead to content overflowing into the gutter and covering the floating ToC.
The problem at: https://twitter.com/mariviere1/status/1589662823378194433 appears to be fixed per #2649:
But the wrapping isn't applied within tables:
````
---
format: html
---
## Accessibility
Really long string below:
| Description | Windows & Linux | Mac |
|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------|:---------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------|
| `Toggle Screen Reader Support` | Alt+Shift+/ | Ctrl+Option+/ |
| `Speak Text Editor Location` | Alt+Shift+1 | Ctrl+Option+1 |
| Focus Console Output | Ctrl+\` or Alt+Shift+2 | Ctrl+\` or Ctrl+Option+2 |
| `Toggle Tab Key Always Moves Focus which is a long sentence and will it ever wrap nope still won't wrap in a table` | Alt+Shift+\[ | Ctrl+Option+\[ |
| Focus Next Pane | F6 | F6 |
| Focus Previous Pane | Shift+F6 | Shift+F6 |
| Focus Main Toolbar | Alt+Shift+Y | Ctrl+Option+Y |
\
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-11-07T18:28:10Z",
"creator": "jthomasmock",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3221,
"state": "closed",
"title": "Long strings in backticks do not wrap",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3221"
} |
```
---
title: Break
---
This will [break quarto](hi.html#oh%20%no).
```
The error message is pretty terrible:
```
quarto render bad-url.qmd
pandoc
to: html
output-file: bad-url.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: Break
ERROR: URIError: URI malformed
URIError: URI malformed
at decodeURI (<anonymous>)
at getDecodedAttribute (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/html.ts:24:12)
at processFileResourceRefs (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/html.ts:128:18)
at resolveResourceTag (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/html.ts:141:3)
at file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/core/html.ts:85:20
at Array.forEach (<anonymous>)
...
``` | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-11-07T18:19:06Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3220,
"state": "closed",
"title": "Invalid URIs cause quarto to fail with bad error message",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3220"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3207
<div type='discussions-op-text'>
<sup>Originally posted by **obrl-soil** November 7, 2022</sup>
Having recently started a Mastodon account, I see there's an option to help 'verify' one's account against one or more external websites, described in the [docs here](https://docs.joinmastodon.org/user/profile/) and more generally [here](http://microformats.org/wiki/rel-me), with results that look [like this](https://mastodon.social/@Mastodon). tl;dr one adds `rel="me"` to the `<a></a>` tag when linking to one's Mastodon profile from elsewhere.
I'm not sure how to do this on my blog's About page except by editing the HTML immediately after rendering the site and before pushing it to GH pages [like this](https://github.com/obrl-soil/obrl-soil.github.io/commit/7aeb06aaf977df0edc35b2a2eb58da9f76de6afb).
Would it be possible to add an attribute to the yml in `about.qmd` to help automate this? e.g.
```
links:
- icon: mastodon
aria-label: Mastodon
href: https://mastodon.social/@yourhandle
rel: "me"
```
There are other variations I've seen like `rel="me nofollow"` that may also need be handled.</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-11-07T13:38:32Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3212,
"state": "closed",
"title": "rel=\"me\" verification on About page links",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3212"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3060
<div type='discussions-op-text'>
<sup>Originally posted by **kir0ul** October 27, 2022</sup>
Hi,
Thanks for this super useful tool!
I was wondering if there's a way to add a `loop="true"` attribute to a `<video>` element in a `reveal.js` presentation?</div> | {
"assignee": "allenmanning",
"comments": 1,
"created_at": "2022-11-07T10:36:34Z",
"creator": "allenmanning",
"is_pull_request": false,
"labels": [
"enhancement",
"good-first-issue",
"video"
],
"locked": false,
"milestone": "v1.4",
"number": 3210,
"state": "open",
"title": "Adding attributes to video shortcodes like looping",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3210"
} |
### Bug description
Hi,
when templating a document structure and adding literature references
```
quarto create-project --type book
cat intro.qmd
# Introduction
@knuth84
# Chapter 2
## Subchap 1
## Subchap 2
### Subsubchap 1
### Subsubchap 2
```
it migtht come to this strange result for all formats:
<img width="732" alt="Bildschirmfoto 2022-11-07 um 11 13 21" src="https://user-images.githubusercontent.com/91615683/200284904-fba85f95-7e74-42d7-9ce5-10e84d242375.png">
Adding a blank line before chapter 2 doesn't lead to this, so I think parsing get's here confused.
```
quarto --version
1.2.258
uname -mrs
Darwin 21.6.0 arm64
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-07T10:21:26Z",
"creator": "iusgit",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3208,
"state": "closed",
"title": "Citation disturbs templated TOC",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3208"
} |
### Bug description
The [documentation](https://quarto.org/docs/books/book-structure.html#parts-appendices) has
```
crossref:
appendix-title: "App."
appendix-delim: ":"
```
as example. `quarto render` gives
```
ERROR: Project _quarto.yml validation failed.
In file _quarto.yml
(line 73, columns 3--17) property name appendix-title is invalid
72: ref-hyperlink: true
73: appendix-title: "Supplement"
~~~~~~~~~~~~~~
ℹ The error happened in location crossref:appendix-title.
```
`quarto check` reports
```
[✓] Checking Quarto installation......OK
Version: 1.2.134
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.9.2
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[✓] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /home/rstudio/R/x86_64-conda-linux-gnu-library/4.1
- /opt/conda/lib/R/library
rmarkdown: 2.16
[✓] Checking Knitr engine render......OK
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-11-07T06:42:22Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 3205,
"state": "closed",
"title": "Property name appendix-title is invalid",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3205"
} |
### Bug description
````md
---
title: "Untitled"
format:
revealjs:
center: true
theme: beige
fig-align: center
filters:
- filters/diagram-generator.lua
- quarto
---
# hello
```{.plantuml width=80%}
@startuml
skinparam backgroundcolor transparent
A -> B : hello
@enduml
```
# hello 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()
```
```{python}
!ls
```
# test bash
```{bash}
ls
```
````
The output of the bash block is not rendered. Why?
Rstudio: 2022.07.2 Build 576
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2022-11-07T04:53:53Z",
"creator": "bayeslearner",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3203,
"state": "closed",
"title": "output of bash block not rendered. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3203"
} |
### Bug description
`quarto render --help` works as expected, displays a typical help menu
The shorthand `quarto render -h` gives
```
ERROR: The specified directory ('.') is not a Quarto project
```
MacOS Monterey, Quarto 1.2.262 installed via .pkg
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-11-07T03:55:19Z",
"creator": "g-simmons",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3202,
"state": "closed",
"title": "quarto render -h throws an error if not inside a quarto project",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3202"
} |
### Bug description
[My blog](https://www.quantumjitter.com/categories/r/) contains some `qmd` posts (with a `hugo-md` format) and some `Rmarkdown`. [This is the repo](https://github.com/cgoo4/quantumjitter).
The [RSS feed](https://simplepie.org/demo/?feed=https%3A%2F%2Fwww.quantumjitter.com) is not behaving as expected: It renders the images (e.g. uploads and ggplots) only for those in `Rmarkdown`. For the quarto posts I get only the text-based content.
IDE Version 2022.12.0-daily+295 (2022.12.0-daily+295) running on macOS Monterey version 12.6
Update 25/11 -- I've rebuilt the site with the html format to make fuller use of all the Quarto features including code-linking and date-modified etc., and to fix the RSS feed.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 0,
"created_at": "2022-11-06T12:02:17Z",
"creator": "cgoo4",
"is_pull_request": false,
"labels": [
"bug",
"hugo"
],
"locked": false,
"milestone": "Future",
"number": 3195,
"state": "open",
"title": "RSS feed missing images using the Quarto `hugo-md` format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3195"
} |
Sir, I was making a class note for students to teach linear model analysis using R. I was making the report in Quarto with knitr engine, and step by step previewing the outputs with following command:
quarto preview 'filename.qmd'
But, when I fitted lm() model and gave summary (km.object) command, then entire HTML preview got disturbed. I think something is not supported, because when I created regular HTML output with command,
quarto preview 'filename.qmd' -- to html
then also that output was distributed. Please help and guide. | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-06T09:47:53Z",
"creator": "aksigkvgithub",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3193,
"state": "closed",
"title": "summary.lm() output disturbs the entire Quarto output with knitr engine",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3193"
} |
### Bug description
I was confused for a while why my project wasn't rendering anymore with no error without me making any changes to it. The reason turned out to be that I had moved the project to a path that had a directory that starts with a `.` (hidden).
I realize ignoring hidden directories *in the project directory* is intended per https://quarto.org/docs/projects/quarto-projects.html#render-targets, but perhaps it was not the intention to ignore everything if a parent directory is hidden? It might seem odd to work under a hidden dir, but in my case it was `~/.julia/dev/`, where Julia package development typically takes place.
A simple way to reproduce (this is on Windows):
```
PS D:\temp\.hidden> quarto create-project myproject
Creating project at D:\temp\.hidden\myproject:
- Created _quarto.yml
- Created myproject.qmd
PS D:\temp\.hidden> quarto render myproject
PS D:\temp\.hidden> quarto -v
1.2.262
```
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 7,
"created_at": "2022-11-05T21:11:52Z",
"creator": "visr",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3186,
"state": "open",
"title": "quarto project render empty if a parent dir is .hidden",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3186"
} |
### Bug description
Using a build obtained an hour ago via `git pull` followed by `./configure.sh`, on Mac, editing in VSCode, watching with Firefox.
I was adding the subscription feature to my blog. I added a `subscribe.html` file and was playing with it. Loaded the blog with `quarto preview` at the command line. I noticed that when editing and saving `subscribe.html` changes do not force an update of the preview in the browser. I guess this means that `subscribe.html` is not among the files monitored for changes during preview, and it would be easier if it were.
Holler if you need more info but I don't this is related to my particular files.
| {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-11-05T17:51:02Z",
"creator": "bryanhanson",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3185,
"state": "open",
"title": "Resource files are not watched in preview mode",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3185"
} |
The citations don't have hyperlinks when output to pdf or word. Other cross-references work as intended. How do I add hyperlinks to the citations? | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-11-05T13:40:39Z",
"creator": "ghost",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.3",
"number": 3197,
"state": "closed",
"title": "Add hyperlinks for citations",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3197"
} |
When I change the format from html to pdf in the getting-started [example](https://quarto.org/docs/get-started/hello/rstudio.html)
I get the error
```
compilation failed- error
Unable to load picture or PDF file 'https://quarto.org/docs/get-started/hello/images/rstudio-hello.png'.
```
When I save the image local it works but I would prefer using the link. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-11-05T10:31:22Z",
"creator": "johannes4998",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 3375,
"state": "closed",
"title": "Auto-resolve external figures in PDF format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3375"
} |
When I render a notebook in quarto within a headless job (OS Shell), the matplotlib figures in the notebook don't have the `img-fluid` class (just `class= "column-page-left"`), and end up covering up the TOC. When I render the notebook manually on the server (Jupyterlab terminal) it looks correct and the images have the `img-fluid` class (`class="column-page-left img-fluid"`).
This is using the same docker file / environment in both cases, the difference is the way the render command is executed.
Is there a way to prevent the figures from covering the TOC?
**Ubuntu 20.04.5 LTS
Kernel version 5.4.217-126.408.amzn2.x86_64
Quarto v1.1.251**
___
`quarto render test.ipynb --execute` (_Jupyterlab terminal_):
<img width="1066" alt="image" src="https://user-images.githubusercontent.com/13021405/200091680-0b863179-037f-46fe-be3a-42ae4e5bd3ff.png">
___
`quarto render test.ipynb --execute` (_Job OS Shell_):
<img width="1237" alt="image" src="https://user-images.githubusercontent.com/13021405/200091801-387d3bbc-58ff-4c72-8a02-074541ac5dd9.png"> | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-05T00:46:47Z",
"creator": "filipj8",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3196,
"state": "closed",
"title": "TOC is covered by figures (flakey)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3196"
} |
### Bug description
When rendering to markdown, if any cell output contains fenced codeblocks, the closing fence characters get escaped (or weirder things happen, if several fenced code blocks appear in a cell output).
I'm seeing this on a mac osx, on quart version `1.1.251`. Note that the examples render to github flavored markdown, but `format: markdown` behaves in similar ways.
## Basic Example
**qmd**
``````md
---
format: gfm
jupyter:
jupytext:
text_representation:
extension: .qmd
format_name: quarto
format_version: '1.0'
jupytext_version: 1.14.1
kernelspec:
display_name: Python 3 (ipykernel)
language: python
name: python3
---
# example
```{python}
def make_codeblock():
return "```python\n1 + 1\n```"
print(make_codeblock())
```
``````
**output**
Note the `` \`\`\` ``
``````md
# example
``` python
def make_codeblock():
return "```python\n1 + 1\n```"
print(make_codeblock())
```
```python
1 + 1
\`\`\`
``````
## Example: multiple code blocks in output
Note that if you run multiple prints, stranger things happen:
**code:**
``````
print(make_codeblock())
print(make_codeblock())
``````
**cell output:**
``````
```python
1 + 1
``` python
1 + 1
```
\`\`\`
``````
## Looks okay in jupyter notebook
<img width="884" alt="image" src="https://user-images.githubusercontent.com/2574498/200058153-9d445d3c-4825-446f-826e-e6a65ebc8a37.png">
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-11-04T19:22:55Z",
"creator": "machow",
"is_pull_request": false,
"labels": [
"bug",
"jupyter"
],
"locked": false,
"milestone": "v1.3",
"number": 3179,
"state": "closed",
"title": "Conversion to markdown incorrectly escapes backticks in printed output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3179"
} |
### Bug description
**Context,** my current workflow is to have a QMD that analyses a model fit using only the fit object.
This is then pulled into a application specific report using `knitr::knit_child`.
**Issue** is that the table of contents (TOC) is missing subsections if the child report has n > 1 subsections.
See the TOC in the following reproducible example.
````
---
format: html
keep-md: true
toc: true
toc-depth: 3
number-sections: true
---
```{r setup}
#| include: false
include_child <- function(n) {
txt <- paste(
sprintf("### H3 (Child) - %s\nSome content\n", seq(n), seq(n)),
collapse = "\n"
)
res <- knitr::knit_child(text = txt, quiet = TRUE)
return(res)
}
```
## Good
Section appears in TOC.
```{r}
#| echo: false
#| results: asis
cat(include_child(n = 1))
```
## Bad
No sections appears in TOC.
```{r}
#| echo: false
#| results: asis
cat(include_child(n = 2))
```
````
I'm using Windows 10 and the following version of RStudio:
> RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) 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
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-11-04T18:36:18Z",
"creator": "nclJoshCowley",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3178,
"state": "open",
"title": "TOC ignoring subsections from child document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3178"
} |
### Bug description
# Configuration
quarto release `1.2.258`
quarto tools:
```
[✓] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Up to date v2022.11 v2022.11
```
OS:
```
Systemversion: macOS 13.0 (22A380)
Kernel-Version: Darwin 22.1.0
```
# Minimal example
I created the following quarto document called `test.qmd`
````{quarto}
---
format:
pdf:
default
---
```{dot}
//| fig-cap: "Caption"
//| label: fig-efa
digraph D {
A [shape=diamond]
B [shape=box]
C [shape=circle]
A -> B [style=dashed, color=grey]
A -> C [color="black:invis:black"]
A -> D [penwidth=5, arrowhead=none]
}
```
````
Subsequently I render the document using the following command from the command line or use the inbuilt quarto render function of the vscode extension.
```{bash}
quarto render test.qmd
```
# Expected behavior
I would expect a PDF document to render, including the graph diagram.
# Actual Behavior
I receive the following error message and no PDF or intermediary files are produced.
````
ERROR: NotFound: No such file or directory (os error 2)
````
# Remarks
Rendering html documents works with the example above when changing
```{yaml}
format:
pdf:
default
```
to
```{yaml}
format:
html:
default
```
in the file `test.qmd`.
Rendering the document without the `dot` code chunk works without problems
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-11-04T18:35:14Z",
"creator": "philwunderlich",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 3177,
"state": "closed",
"title": "Improve error message when Chrome and Chromium are not installed",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3177"
} |
### Bug description
When scrolling on a quarto website, e.g. https://quarto.org/, the navbar is meant to disappear and appear on scrolling.
Every time this happens, a style tag is added to the head:
```
section:target::before {
content: "";
display: block;
height: 66px;
margin: -66px 0 0;
}
```
I am not sure what, but something is not right here.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-11-04T15:28:02Z",
"creator": "jmbuhr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 3172,
"state": "closed",
"title": "navbar hiding and appearing adds infinitely many `style` tags to html `head`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3172"
} |
### Bug description
I am having trouble when trying to reproduce the examples in the [docs](https://quarto.org/docs/interactive/ojs/data-sources.html) on how to use arrow as a data source for Quarto. Below is a reprex and the error message I am getting.
````
---
title: "Quarto with arrow"
format:
html:
self-contained: true
---
```{r}
arrow::write_feather(
mtcars,
"data.arrow",
compression = "uncompressed"
)
```
```{ojs}
data = FileAttachment("data.arrow").arrow()
Inputs.table(data)
```
````
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
I am running a Windows machine.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 12,
"created_at": "2022-11-04T15:20:03Z",
"creator": "novotny1akub",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3171,
"state": "closed",
"title": "Quarto with arrow",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3171"
} |
Hi,
when I create a book project like the default with `quarto create-project --type book` and add an appendix like
```
project:
type: book
book:
title: "quartoiusbook"
author: "Jane Doe"
date: "3.11.2022"
chapters:
- index.qmd
- intro.qmd
- summary.qmd
- references.qmd
appendices:
- Appendix_01.qmd
bibliography: references.bib
format:
html:
theme: cosmo
pdf:
documentclass: scrreprt
```
then I end-up with the wrong page number in the TOC for the additional entry of "Appendices" (should be page 7 and not 6):
<img width="867" alt="Bildschirmfoto 2022-11-04 um 12 03 59" src="https://user-images.githubusercontent.com/91615683/199957947-3d4ee2ca-241b-4517-ac6b-4d7a910a8390.png">
This is caused here:
https://github.com/quarto-dev/quarto-cli/blob/346d80e55abc83e0a5b87e93a17730eac5656a92/src/resources/filters/quarto-pre/book-numbering.lua#L28
The reason – as I understand it – is that before a new chapter in KOMA etc is added a `\cleardoublepage` is done. The `\addcontentsline` does not see this. Whenever I create book documents with latex I add
```
\cleardoublepage
\phantomsection
\addcontentsline{toc}{part}{TOC entry title}
```
Note, that `\phantomsection` is needed to throw an anchor for the hyperlink, which otherwise would lead to the wrong page...
Can we extend the mentioned code like? E.g.
```
local appendixPara = pandoc.Para({
pandoc.RawInline('latex', '\\cleardoublepage\n\\phantomsection\n\\addcontentsline{toc}{part}{')
})
tappend(appendixPara.content, el.content)
appendixPara.content:insert(pandoc.RawInline('latex', '}\n\\appendix'))
```
Cheers,
Maarten | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-04T11:19:56Z",
"creator": "iusgit",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3164,
"state": "closed",
"title": "Wrong page number in the TOC for \"Appendices\"",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3164"
} |
### Bug description
I tried to use Quarto with a sqlite database, but it does not seem to be working. Below is an error message I get when I open the generated html file in the browser. The reprex is also below. [Here ](https://observablehq.com/d/a9047fb68f840243)is an observablehq workbook where this sqlite database works with no issues. I assume this happens because sqlite.js is not loaded in Quarto whilst in observablehq, it is a part of their standard library. In addition, Quarto [documentation ](https://quarto.org/docs/interactive/ojs/data-sources.html) links [observablehq/stdlib](https://github.com/observablehq/stdlib#attachment_sqlite) which I think is rather unfortunate because the examples from there need to be first translated to ojs dialect of JavaScript. For example, the observablehq/stdlib documentation mentions this code `const db = await FileAttachment("chinook.db").sqlite();`, which contains the const, which is not used in Quarto context I believe.
````
---
title: "Quarto with sqlite database"
format:
html:
self-contained: true
mode: visual
---
```{r include=F}
library(DBI)
n <- 10000
df <- data.frame(
cat = letters[1:2] |> sample(size = n, replace = T),
num = runif(n)
)
con <- dbConnect(RSQLite::SQLite(), "sqlite.db")
dbWriteTable(con, "table", df, overwrite = T)
dbDisconnect(con)
```
```{ojs}
//| echo: false
db = await FileAttachment("sqlite.db").sqlite();
```
````
Windows operating system
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 11,
"created_at": "2022-11-04T10:20:08Z",
"creator": "novotny1akub",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "v1.2",
"number": 3163,
"state": "closed",
"title": "Quarto with SQLite does not seem to be working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3163"
} |
It seems that paths beginning with `/` are treated as relative paths.
For example when running quarto 1.2.258, with this content in aquarto project in `/home/user/Documents/Boulot/`:
```md
---
format:
latex:
papersize: a5
classoption:
- fontsize=10pt
- DIV=calc
---
# Exercices sur le chapitre 2: Représentation des entiers relatifs
{{< include /home/user/_file.qmd >}}
```
Gives this error:
```
ERROR: Include directive failed.
in file ...,
could not find file /home/user/Documents/Boulot/home/user/_file.
```
| {
"assignee": null,
"comments": 1,
"created_at": "2022-11-03T18:10:40Z",
"creator": "benabel",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3160,
"state": "closed",
"title": "Can't include file with absolute path with include directive",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3160"
} |
Dear developers of quarto,
running quarto with this content:
```md
---
format:
latex:
papersize: a5
classoption:
- fontsize=10pt
- DIV=calc
---
# Exercices sur le chapitre 2: Représentation des entiers relatifs
{{< include ./_file with space.qmd >}}
```
Outputs this error in `quarto 1.2.258`
```
ERROR: Include directive failed.
in file /home/ben/Documents/Boulot/1NSI/2-Représentation des données : types et valeurs de base/P2C2-TD-Representation-des-entiers-relatifs-ORIGINAL.qmd,
could not find file /home/ben/Documents/Boulot/1NSI/2-Représentation des données : types et valeurs de base/_file.
```
Quarto is searching for `_file` instead of `_file with space.qmd`.
| {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-11-03T18:01:51Z",
"creator": "benabel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3159,
"state": "closed",
"title": "Can't include file with space with include directive",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3159"
} |
### Bug description
In the `_quarto.yml` file, setting `engine: knitr` or any variants (`jupyter: python3`, etc) should apply as the default for any files unless modified in the subsequent file's YAML.
On M1 Pro Mac running MacOS Monteray.
Using RStudio Version 2022.12.0-preview+303 (2022.12.0-preview+303)
Quarto v1.2.242
Reprex:
1. Create a project
```bash
quarto create-project test-engine
```
2. Set `engine: knitr` in the `_quarto.yml`
```yaml
project:
type: website
website:
title: "test-engine"
navbar:
left:
- href: index.qmd
text: Home
- about.qmd
format:
html:
theme: cosmo
css: styles.css
toc: true
engine: knitr #<- this is the change
```
2. Change a chunk in the `index.qmd` to `python`:
````
```{python}
1+1
```
````
3. `quarto render`
The render of `index.qmd` is executed within a Jupyter kernel instead of `knitr` + `reticulate` even with the `engine: knitr` set at global/`_quarto.yml` level.
The correct behavior would be to use `knitr` since that is set at the global level.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-11-03T17:19:57Z",
"creator": "jthomasmock",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3157,
"state": "open",
"title": "engine: should be respected globally at the _quarto.yml level",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3157"
} |
Consider the following code:
````
---
title: "Untitled"
format: pdf
engine: jupyter
---
```{python}
#| echo: false
#| fig-align: center
#| fig-width: 2
import matplotlib.pyplot as plt
x = [1, 2]
y = [2, 3]
plt.plot(x,y)
```
````
The chosen value for `fig-width` has no effect. I am using Quarto in RStudio.
| {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-11-03T12:51:05Z",
"creator": "psads-git",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3155,
"state": "open",
"title": "fig-width has no effect with jupyter engine",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3155"
} |
### Bug description
We can convert between .ipynb and .qmd representations of a notebook using the quarto convert command.
However, some notebooks have custom directives. These are normally supported during project compilation using the `ipynb-filters` option in `_quarto.yml` and are essential to the nbdev project where directives such as `#|export` select code cells for compilation into a python library.
`quarto convert` doesn't work on notebooks designed to make use of this advanced feature.
If an ipynb file had the code cell:
```python
#| export
import numpy as np
```
converting it into QMD will produce the cell:
```python
#| '0': e
#| '1': x
#| '2': p
#| '3': o
#| '4': r
#| '5': t
import numpy as np
```
and converting back will discard the directive completely:
```python
import numpy as np
```
Starting out with a correct `#|export` directive in the QMD version of the file and attempting to convert the file into ipynb produces the following error:
```
> ERROR: TypeError: Cannot delete property '0' of [object String]
```
Ideally what would happen during a round-trip conversion is that the directives included at the top of code cells are preserved, just as natively supported directives are presented.
If quarto convert or some other tool could handle the round trip conversion between ipynb and qmd more cleanly, then nbdev projects and other tools utilizing the advanced nb-filter feature could use qmd source files for their work instead of jupyter notebooks! And the advantages of QMD over IPYNB as a format for work mixing text and code probably don't need to be outlined here.
Simple example file that quarto convert will struggle with:
https://gist.githubusercontent.com/githubpsyche/32c6391c30699bfd103b4992743b0af3/raw/a17f651cc28a9bb4f3afeab14bb9259ebc0bd0f6/example.ipynb
Using Windows 11. I believe I've tried this with the current release 1.1.251 and 1.2.253.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 13,
"created_at": "2022-11-03T08:50:05Z",
"creator": "githubpsyche",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3152,
"state": "closed",
"title": "custom directives / ipynb-filters during quarto convert",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3152"
} |
### Bug description
Hi!
I have a website with control version in GitHub. I want to include a CI process to render it every time I push something.
Following the docs for GitHub pages (https://quarto.org/docs/publishing/github-pages.html#github-action) I copy-pasted this into `.github/workflows/publish.yml`
```yaml
on:
workflow_dispatch:
push:
branches: [ main ]
pull_request:
types: [ closed ]
name: Quarto Publish
jobs:
build-deploy:
runs-on: ubuntu-latest
permissions:
contents: write
steps:
- name: Check out repository
uses: actions/checkout@v2
- name: Set up Quarto
uses: quarto-dev/quarto-actions/setup@v2
with:
version: pre-release
- name: Render and Publish
uses: quarto-dev/quarto-actions/publish@v2
with:
target: gh-pages
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
```
However, I'm getting this error in every action in the `Render and Publish` part
```
ERROR: No _publish.yml file available (_publish.yml specifying a destination required for non-interactive publish)
Error: Process completed with exit code 1.
```
The full output is here
<details>
```
Run quarto-dev/quarto-actions/publish@v2
with:
target: gh-pages
GITHUB_EMAIL: [email protected]
GITHUB_USERNAME: Quarto GHA Workflow Runner
path: .
render: true
env:
BUNDLE_EXT: linux-amd64.deb
GITHUB_TOKEN: ***
Run git config --global user.email "[email protected]"
git config --global user.email "[email protected]"
git config --global user.name "Quarto GHA Workflow Runner"
TARGET=""
if [ "$TARGET" == "" ]; then
TARGET="gh-pages"
fi
if [ "true" != "true" ]; then
quarto publish $TARGET . --no-render
else
quarto publish $TARGET .
fi
shell: /usr/bin/bash --noprofile --norc -e -o pipefail {0}
env:
BUNDLE_EXT: linux-amd64.deb
GITHUB_TOKEN: ***
CONNECT_SERVER:
CONNECT_API_KEY:
NETLIFY_AUTH_TOKEN:
QUARTO_PUB_AUTH_TOKEN:
ERROR: No _publish.yml file available (_publish.yml specifying a destination required for non-interactive publish)
Error: Process completed with exit code 1.
```
</details>
Netlify requires a `_publish.yml` to work properly, but there is no documentation about this file for GitHub.
Am I making some mistake somewhere?
Thanks in advance.
Best.
**System:**
- quarto Version: 1.2.256
- OS: MacOS 13.0
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-02T10:29:43Z",
"creator": "maikol-solis",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3147,
"state": "closed",
"title": "ERROR: No _publish.yml file available for GitHub pages CI",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3147"
} |
Thank you all in advance, for being here, for Quarto, and for reading this.
I am going to ask this in the _Citation Style Language forum_ too.
I am using the **Quarto** version that came installed with the latest release of **RStudio**, in Windows 11.
```{markdown}
Spotted Wakerobin" Release (e7373ef8, 2022-09-06) 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}
> quarto::quarto_version()
[1] ‘1.1.189’
```
# Issue description
I am facing many problems with Quarto. One of those is that I am currently having to use a custom _.csl_ file to style my citations in order to comply with my institution's annoying rules, but it does not seem to work as expected.
For instance, take into account that I have to cite **inside two different _footnotes_** (yes, I have to cite sources in footnotes) _pages 1 to 10_ and then _pages 11 to 17_ of the following article
```{tex}
@article{commenges_statistical_2009,
title = {Statistical models: {Conventional}, penalized and hierarchical likelihood},
volume = {3},
issn = {1935-7516},
shorttitle = {Statistical models},
url = {https://projecteuclid.org/journals/statistics-surveys/volume-3/issue-none/Statistical-models-Conventional-penalized-and-hierarchical-likelihood/10.1214/08-SS039.full},
doi = {10.1214/08-SS039},
number = {none},
urldate = {2022-11-01},
journal = {Statistics Surveys},
author = {Commenges, Daniel},
year = {2009},
}
```
and that, concerning citation abbreviations, in the `locale` block of my _.csl_ file I have (*please, notice the _short_ and _long_ abbreviations forms*)
```
<locale xml:lang="it-IT">
<terms>
<term name="page" form="short">
<single>p.</single>
<multiple>pp.</multiple>
</term>
<term name="translator" form="verb-short">tr. it. di</term>
<term name="no date">s.d.</term>
<term name="ibid" form="short">ivi</term>
<term name="ibid" form="long">ibidem</term>
<term name="cited" form="short">cit.</term>
<term name="cited" form="long">op.cit.</term>
<term name="issue" form="short">fasc.</term>
<term name="season-01">primavera</term>
<term name="season-02">estate</term>
<term name="season-03">autunno</term>
<term name="season-04">inverno</term>
</terms>
</locale>
```
Hence, I create a footnote (Ctrl + Alt + F7) alongside the end of the related paragraph, and then type
```{markdown}
@commenges_statistical_2009, pp. 1-10.
```
So, I make another footnote and type
```{markdown}
@commenges_statistical_2009, pp. 11-17.
```
## Actual behaviour
I get (please, notice the *_short shaped_* abbreviation *cit.* in the **second citation**, and that there is no space between the abbreviation and the quotation glyph ``>>'' ) the following
```
> D. COMMENGES, Statistical models: Conventional, penalized and hierarchical likeli-
hood, «Statistics Surveys», vol. 3, fasc. none, 2009, https://projecteuclid.org/journals
/statistics-surveys/volume-3/issue-none/Statistical-models-Conventional-penalized-
and-hierarchical-likelihood/10.1214/08-SS039.full, pp. 1-1
> D. Commenges, «Statistical models»cit., pp. 1-17.
```
## Expected behaviour
I get (please, notice the *_long shaped_* abbreviation *op. cit.* in the **second citation**, and that there is a blank space between the abbreviation itself and the quotation glyph ``>>'') the following
```
> D. COMMENGES, Statistical models: Conventional, penalized and hierarchical likeli-
hood, «Statistics Surveys», vol. 3, fasc. none, 2009, https://projecteuclid.org/journals
/statistics-surveys/volume-3/issue-none/Statistical-models-Conventional-penalized-
and-hierarchical-likelihood/10.1214/08-SS039.full, pp. 1-1
> D. Commenges, «Statistical models» op.cit., pp. 1-17.
```
# Question
How to deal with such an issue?
Do I have to modify something in _.csl_ file or do I have, perhaps, to specify something to get the *_long form_* of the abbreviation (_op.cit_ instead of _cit._).
Moreover, is there a way for one to make use of the handy abbreviation *_ibidem_* (or *_ivi_*, as per the short form in this .csl)?
I am asking this additional question too because it is not clear how one could specify same resource with same pages in two different citations and get the supposed abbreviation _ibidem_ as a replacement for a matching citation following the first.
## The .csl file itself
Hereby follows the _.csl_ I am using in Quarto specifying it in the proper `YML` field, which I got modifying the one named [_Quaderni Materialisti (Italiano)_](https://editor.citationstyles.org/styleInfo/?styleId=http%3A%2F%2Fwww.zotero.org%2Fstyles%2Fquaderni-materialisti).
```{XML}
<?xml version="1.0" encoding="utf-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" class="note" version="1.0" default-locale="it-IT" demote-non-dropping-particle="sort-only">
<!-- This style was edited with the Visual CSL Editor (https://editor.citationstyles.org/visualEditor/) -->
<info>
<title>Quaderni Materialisti (Italiano)</title>
<id>http://www.zotero.org/styles/quaderni-materialisti</id>
<link href="http://www.zotero.org/styles/quaderni-materialisti" rel="self"/>
<link href="http://www.zotero.org/styles/universita-di-bologna-lettere" rel="template"/>
<link href="http://www.quadernimaterialisti.unimib.it/?p=107" rel="documentation"/>
<author>
<name>Patrick O'Brien</name>
</author>
<category citation-format="note"/>
<category field="humanities"/>
<category field="linguistics"/>
<category field="philosophy"/>
<issn>1972-3792</issn>
<updated>2022-09-14T21:23:48+00:00</updated>
<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
</info>
<locale xml:lang="it-IT">
<terms>
<term name="page" form="short">
<single>p.</single>
<multiple>pp.</multiple>
</term>
<term name="translator" form="verb-short">tr. it. di</term>
<term name="no date">s.d.</term>
<term name="ibid" form="short">ivi</term>
<term name="ibid" form="long">ibidem</term>
<term name="cited" form="short">cit.</term>
<term name="cited" form="long">op.cit.</term>
<term name="issue" form="short">fasc.</term>
<term name="season-01">primavera</term>
<term name="season-02">estate</term>
<term name="season-03">autunno</term>
<term name="season-04">inverno</term>
</terms>
</locale>
<macro name="editor-translator">
<group delimiter=", ">
<choose>
<if variable="author">
<names variable="editor" delimiter=", ">
<name initialize-with=". "/>
<label form="verb" text-case="lowercase" prefix=" (" suffix=") " strip-periods="true"/>
</names>
<choose>
<if variable="container-author">
<group>
<text term="in" text-case="lowercase" suffix=" "/>
<names variable="container-author">
<name initialize-with=". "/>
</names>
</group>
</if>
</choose>
</if>
</choose>
<choose>
<if variable="author editor" match="any">
<choose>
<if match="none" variable="original-title">
<names variable="translator" delimiter=", ">
<label form="verb-short" text-case="lowercase" strip-periods="true" prefix=" "/>
<name prefix=" "/>
</names>
</if>
</choose>
</if>
</choose>
</group>
</macro>
<macro name="secondary-contributors">
<choose>
<if type="chapter paper-conference" match="none">
<text macro="editor-translator"/>
</if>
</choose>
</macro>
<macro name="container-contributors">
<choose>
<if type="chapter paper-conference" match="any">
<text macro="editor-translator"/>
</if>
</choose>
</macro>
<macro name="editor-note">
<names variable="editor">
<name initialize-with=". "/>
<label form="verb" prefix=" (" suffix=")" strip-periods="true"/>
</names>
</macro>
<macro name="translator-note">
<names variable="translator">
<name sort-separator=", " delimiter=", "/>
<label form="verb-short" prefix=", "/>
</names>
</macro>
<macro name="recipient-note">
<names variable="recipient" delimiter=", ">
<label form="verb" prefix=" " text-case="lowercase" suffix=" "/>
<name and="text" delimiter=", "/>
</names>
</macro>
<macro name="contributors-note">
<names variable="author" font-variant="small-caps">
<name initialize-with=". "/>
<substitute>
<text macro="editor-note"/>
<text macro="translator-note"/>
</substitute>
</names>
<text macro="recipient-note"/>
</macro>
<macro name="editor">
<names variable="editor">
<name delimiter-precedes-last="always" initialize-with=". " name-as-sort-order="first"/>
<label form="verb" strip-periods="false" prefix=" (" suffix=")"/>
</names>
</macro>
<macro name="translator">
<names variable="translator">
<name name-as-sort-order="first" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
<label form="verb-short" prefix=" (" suffix=")"/>
</names>
</macro>
<macro name="recipient">
<choose>
<if type="personal_communication">
<choose>
<if variable="genre">
<text variable="genre" text-case="capitalize-first"/>
</if>
<else>
<text term="letter" text-case="capitalize-first"/>
</else>
</choose>
</if>
</choose>
<text macro="recipient-note" prefix=" "/>
</macro>
<macro name="contributors">
<names variable="author" font-variant="small-caps">
<name delimiter-precedes-last="always" initialize-with=". " name-as-sort-order="first"/>
<substitute>
<text macro="editor"/>
<text macro="translator"/>
</substitute>
</names>
<text macro="recipient" prefix=". "/>
</macro>
<macro name="recipient-short">
<names variable="recipient">
<label form="verb" prefix=" " text-case="lowercase" suffix=" "/>
<name form="short" and="text" delimiter=", "/>
</names>
</macro>
<macro name="contributors-short">
<names variable="author">
<name form="long" initialize-with="." delimiter=", "/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
</substitute>
</names>
<text macro="recipient-short"/>
</macro>
<macro name="contributors-sort">
<names variable="author">
<name name-as-sort-order="all" and="text" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
</substitute>
</names>
</macro>
<macro name="interviewer-note">
<names variable="interviewer" delimiter=", ">
<label form="verb" prefix=" " text-case="lowercase" suffix=" "/>
<name and="text" delimiter=", "/>
</names>
</macro>
<macro name="interviewer">
<names variable="interviewer" delimiter=", ">
<label form="verb" prefix=" " text-case="capitalize-first" suffix=" "/>
<name and="text" delimiter=", "/>
</names>
</macro>
<macro name="title-note">
<choose>
<if variable="title" match="none">
<text variable="genre"/>
</if>
<else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter=", ">
<text macro="original-note"/>
<text variable="title" font-style="italic"/>
</group>
</else-if>
<else>
<text variable="title" quotes="false" font-style="italic"/>
</else>
</choose>
</macro>
<macro name="title">
<choose>
<if variable="title" match="none">
<choose>
<if type="personal_communication" match="none">
<text variable="genre" text-case="capitalize-first"/>
</if>
</choose>
</if>
<else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<group delimiter=", ">
<text macro="original"/>
<text variable="title" font-style="italic"/>
</group>
</else-if>
<else>
<text variable="title" quotes="false" font-style="italic"/>
</else>
</choose>
</macro>
<macro name="title-short">
<choose>
<if disambiguate="true">
<choose>
<if variable="title" match="none">
<choose>
<if type="interview">
<text term="interview" text-case="lowercase"/>
</if>
<else-if type="manuscript speech" match="any">
<text variable="genre" form="short"/>
</else-if>
<else-if type="personal_communication">
<text macro="issued"/>
</else-if>
</choose>
</if>
<else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<text variable="title" form="short"/>
</else-if>
<else>
<text variable="title" form="short" quotes="true"/>
</else>
</choose>
<text term="cited" form="short"/>
</if>
<else>
<text term="cited" form="long" font-style="italic"/>
</else>
</choose>
</macro>
<macro name="description-note">
<group delimiter=", ">
<text macro="interviewer-note"/>
<text variable="medium"/>
<choose>
<if variable="title" match="none"/>
<else-if type="thesis speech" match="any"/>
<else>
<text variable="genre"/>
</else>
</choose>
</group>
</macro>
<macro name="description">
<group delimiter=", ">
<group delimiter=". ">
<text macro="interviewer"/>
<text variable="medium" text-case="capitalize-first"/>
</group>
<choose>
<if variable="title" match="none"/>
<else-if type="thesis speech" match="any"/>
<else>
<text variable="genre" text-case="capitalize-first"/>
</else>
</choose>
</group>
</macro>
<macro name="container-title">
<choose>
<if type="legal_case" match="none">
<text variable="container-title" quotes="true" font-style="italic"/>
</if>
</choose>
</macro>
<macro name="collection-title">
<text variable="collection-title"/>
<text variable="collection-number" prefix=" "/>
</macro>
<macro name="locators">
<choose>
<if type="article-journal">
<group delimiter=" " prefix=", ">
<text term="volume" form="short"/>
<text variable="volume"/>
</group>
<group prefix=", ">
<text term="issue" form="short" suffix=" "/>
<number variable="issue"/>
</group>
</if>
<else-if type="legal_case">
<text variable="volume" prefix=", "/>
<text variable="container-title" prefix=" "/>
<text variable="page" prefix=" "/>
<text variable="locator" prefix=", "/>
</else-if>
<else-if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song" match="any">
<group prefix=", " delimiter=", ">
<group>
<text term="volume" form="short" suffix=" "/>
<number variable="volume" form="roman"/>
</group>
<choose>
<if variable="locator" match="none">
<group>
<number variable="number-of-volumes" form="numeric"/>
<text term="volume" form="short" prefix=" " plural="true"/>
</group>
</if>
</choose>
</group>
</else-if>
</choose>
</macro>
<macro name="locators-newspaper">
<choose>
<if type="article-newspaper">
<group delimiter=", ">
<group delimiter=" ">
<text variable="edition"/>
<text term="edition"/>
</group>
<group>
<text term="section" form="short" suffix=" "/>
<text variable="section"/>
</group>
</group>
</if>
</choose>
</macro>
<macro name="event">
<group>
<text term="presented at" suffix=" "/>
<text variable="event"/>
</group>
</macro>
<macro name="publisher">
<group delimiter=", ">
<text variable="publisher-place"/>
<text variable="publisher"/>
</group>
</macro>
<macro name="issued">
<choose>
<if variable="issued">
<choose>
<if type="graphic report" match="any">
<date variable="issued">
<date-part name="month" suffix=" "/>
<date-part name="day" suffix=", "/>
<date-part name="year"/>
</date>
</if>
<else-if type="legal_case">
<text variable="authority" suffix=" "/>
<date variable="issued">
<date-part name="year"/>
</date>
</else-if>
<else-if type="bill book chapter graphic legal_case legislation motion_picture paper-conference report song thesis" match="any">
<date variable="issued">
<date-part name="year"/>
</date>
</else-if>
<else-if type="article-journal">
<date variable="issued">
<date-part name="month" text-case="lowercase" suffix=" "/>
<date-part name="year"/>
</date>
</else-if>
<else>
<date variable="issued">
<date-part name="month" text-case="lowercase" suffix=" "/>
<date-part name="day" suffix=", "/>
<date-part name="year"/>
</date>
</else>
</choose>
</if>
<else>
<text term="no date" form="short"/>
</else>
</choose>
</macro>
<macro name="point-locators-subsequent">
<group>
<choose>
<if locator="page" match="none">
<choose>
<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<choose>
<if variable="volume">
<group>
<text term="volume" form="short" text-case="lowercase" suffix=" "/>
<number variable="volume" form="numeric"/>
<label variable="locator" form="short" prefix=", " suffix=" "/>
</group>
</if>
<else>
<label variable="locator" form="short" suffix=" "/>
</else>
</choose>
</if>
</choose>
</if>
<else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
<number variable="volume" form="numeric" suffix=":"/>
</else-if>
</choose>
<text variable="locator"/>
</group>
</macro>
<macro name="point-locators">
<choose>
<if variable="locator" match="none">
<text macro="pages"/>
</if>
<else-if type="article-journal">
<text variable="locator" prefix=": "/>
</else-if>
<else-if type="legal_case"/>
<else>
<group prefix=", ">
<choose>
<if locator="page" match="none">
<label variable="locator" form="short" suffix=" "/>
</if>
</choose>
<label variable="locator" form="short" suffix=" "/>
<text variable="locator"/>
</group>
</else>
</choose>
</macro>
<macro name="pages">
<label variable="page" form="short" prefix=", " suffix=" "/>
<text variable="page"/>
</macro>
<macro name="locators-chapter">
<choose>
<if type="chapter paper-conference" match="any">
<choose>
<if variable="page">
<text variable="volume" suffix=":"/>
<text variable="page"/>
</if>
</choose>
</if>
</choose>
</macro>
<macro name="locators-journal">
<choose>
<if type="article-journal">
<label variable="page" form="short" prefix=", " suffix=" "/>
<text variable="page"/>
</if>
</choose>
</macro>
<macro name="archive-note">
<group delimiter=", ">
<text variable="archive_location"/>
<text variable="archive"/>
<text variable="archive-place"/>
</group>
</macro>
<macro name="archive">
<group delimiter=". ">
<text variable="archive_location" text-case="capitalize-first"/>
<text variable="archive"/>
<text variable="archive-place"/>
</group>
</macro>
<macro name="issue">
<choose>
<if type="article-journal legal_case" match="any">
<text macro="issued" prefix=", "/>
</if>
<else-if variable="publisher-place publisher" match="any">
<group prefix=", " delimiter=", ">
<group delimiter=", ">
<choose>
<if variable="title" match="none"/>
<else-if type="thesis speech" match="any">
<text variable="genre"/>
</else-if>
</choose>
<text macro="event"/>
</group>
<text macro="publisher"/>
<text macro="issued"/>
</group>
</else-if>
<else>
<text macro="issued" prefix=", "/>
</else>
</choose>
</macro>
<macro name="access-note">
<group delimiter=", ">
<choose>
<if type="graphic report" match="any">
<text macro="archive-note"/>
</if>
<else-if type="article-journal article-magazine article-newspaper bill book chapter graphic legal_case legislation motion_picture paper-conference report song thesis" match="none">
<text macro="archive-note"/>
</else-if>
</choose>
<choose>
<if type="legal_case" match="none">
<text variable="URL"/>
</if>
</choose>
</group>
</macro>
<macro name="access">
<group delimiter=". ">
<choose>
<if type="graphic report" match="any">
<text macro="archive"/>
</if>
<else-if type="article-journal article-magazine article-newspaper bill book chapter graphic legal_case legislation motion_picture paper-conference report song thesis" match="none">
<text macro="archive"/>
</else-if>
</choose>
<choose>
<if type="legal_case" match="none">
<text variable="URL"/>
</if>
</choose>
</group>
</macro>
<macro name="original-note">
<group delimiter=", ">
<text variable="original-title" font-style="italic"/>
<text variable="original-publisher-place"/>
<text variable="original-publisher"/>
<date form="text" variable="original-date"/>
<names variable="translator">
<label form="verb-short" suffix=" "/>
<name/>
</names>
</group>
</macro>
<macro name="original">
<group delimiter=", ">
<text variable="original-title"/>
<text variable="original-publisher-place"/>
<text variable="original-publisher"/>
<date form="text" variable="original-date"/>
<names variable="translator">
<label form="verb-short" suffix=" "/>
<name initialize-with=". "/>
</names>
</group>
</macro>
<citation et-al-min="4" et-al-use-first="1">
<layout delimiter="; " suffix=".">
<choose>
<if position="ibid-with-locator">
<group delimiter=", ">
<text term="ibid" form="long" text-case="capitalize-first" font-style="italic"/>
<text macro="point-locators-subsequent"/>
</group>
</if>
<else-if position="ibid">
<text term="ibid" form="short" text-case="capitalize-first" font-style="italic"/>
</else-if>
<else-if position="subsequent">
<group delimiter=", ">
<text macro="contributors-short"/>
<text macro="title-short"/>
<text macro="point-locators-subsequent"/>
</group>
</else-if>
<else>
<group delimiter=", ">
<text macro="contributors-note"/>
<text macro="title-note"/>
<text macro="description-note"/>
<text macro="secondary-contributors"/>
<text macro="container-contributors"/>
<text macro="container-title"/>
</group>
<text macro="locators"/>
<text macro="collection-title" prefix=", "/>
<text macro="issue"/>
<text macro="locators-newspaper" prefix=", "/>
<text macro="access-note" prefix=", "/>
<text macro="point-locators"/>
</else>
</choose>
</layout>
</citation>
<bibliography hanging-indent="true" et-al-min="11" et-al-use-first="7" subsequent-author-substitute="———" entry-spacing="0">
<sort>
<key macro="contributors-sort"/>
<key variable="title"/>
<key variable="genre"/>
<key variable="issued"/>
</sort>
<layout suffix=".">
<group delimiter=", ">
<text macro="contributors"/>
<text macro="title"/>
<text macro="description"/>
<text macro="secondary-contributors"/>
<group delimiter=", ">
<text macro="container-contributors"/>
<text macro="container-title"/>
<text macro="locators-chapter"/>
</group>
</group>
<text macro="locators"/>
<text macro="collection-title" prefix=". "/>
<text macro="issue"/>
<text macro="locators-newspaper" prefix=", "/>
<text macro="locators-journal"/>
<text macro="access" prefix=". "/>
</layout>
</bibliography>
</style>
```
Thank you all once more!
_Nicholas_
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 7,
"created_at": "2022-11-01T15:13:50Z",
"creator": "Nicholas-R-Sheriff",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.4",
"number": 3131,
"state": "closed",
"title": "How to handle .CSL's format and abbreviations (like *ibidem*, *op.cit.*, etc.) for .pdf output?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3131"
} |
### Bug description
I am trying to create a report, which should also have List of Figures. However, I am unable to add the plots created by ggplot2 package in the list of figures. In the rendered report, I can see there is a List of Tables and a List of Figures, but the List of Figures is empty. Even though I have created a plot, and added label and caption to that plot, the list remains empty. A minimal example is as follows:
YAML Head
```
---
title: "mtcars"
format:
pdf:
documentclass: scrreprt
fig-align: center
fig-width: 6
fig-height: 5
fig-pos: 'h'
fig-cap-location: bottom
tbl-cap-location: top
pdf-engine: lualatex
keep-tex: true
linestretch: 1.5
toc: true
toc-depth: 2
toc-title: Contents
lof: true
lot: true
number-sections: true
number-depth: 6
colorlinks: true
callout-appearance: simple
callout-icon: true
execute:
echo: false
message: false
warning: false
editor: visual
---
```
Code for Plot
```
{r plot}
#|label: fig-mtcars
#|fig-cap: "A Sample Plot"
library(ggplot2)
ggplot(mtcars, aes(cyl,mpg)) + ggtitle("MPG vs CYL") + geom_point()
```
I have also tried to add the caption manually inside ggplot, using the code below.
```
{r plot}
#|label: fig-mtcars
#|fig-cap: "A Sample Plot"
library(ggplot2)
ggplot(mtcars, aes(cyl,mpg)) + ggtitle("MPG vs CYL") + geom_point() + labs(caption = "Sample Caption")
```
But when I render, the List of Figures remains empty. In the expected output, I should have this plot in the List of Figures. I am using the latest daily build version of RStudio (2022.12.0 - preview +298) and the Quarto version is 1.2.253. The OS is Windows 10.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-01T06:06:49Z",
"creator": "bhattmaulik",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3128,
"state": "closed",
"title": "I am unable to add a plot in the List of Figures in PDF output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3128"
} |
When i use layout: full, the right margin is not going interactive. I can't make any click over there, i tried to reach how to solve it but the only way is taking out the layout function | {
"assignee": null,
"comments": 4,
"created_at": "2022-11-01T01:00:42Z",
"creator": "Felipepereyra",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3129,
"state": "closed",
"title": "YAML => problem with layout: full",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3129"
} |
I tried to render pdf with number-offset. The document seemed to run, but produced the error message:
Aeson exception:
Error in $: parsing [] failed, expected Array, but encountered Number
When I changed output to html or removed number-offset, the code worked. A short .qmd script that produced the error is below:
```
---
title: "Title"
author: "Author"
format:
pdf:
number-sections: true
number-offset: -1
---
## Introduction
## The Methods
### Loading Data
### Computing methods
## Results
```
FYI, I am using quarto on a 64-bit Windows 11 machine, and the LaTeX installation is tinytex.
| {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-10-31T23:21:26Z",
"creator": "thedabs91",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3126,
"state": "closed",
"title": "number-offset does not work with pdf output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3126"
} |
### Bug description
Using Quarto v1.2.253, the following document does not display affiliation header/label.
```
---
title: "Hello world"
author:
- name: Bill Gates
orcid: 0000-0003-1689-0557
email: [email protected]
affiliations:
- name: Bill & Melinda Gates Foundation
address: 440 5th Ave N
city: Seattle
state: WA
postal-code: 98109-4631
format: html
---
```
For some reason, the affiliation label is empty.
<img width="1403" alt="image" src="https://user-images.githubusercontent.com/8896044/199118843-191b7705-0389-4c21-bcba-58c50fd37c48.png">
From Quarto v1.1.251
<img width="1401" alt="image" src="https://user-images.githubusercontent.com/8896044/199119123-06190c2c-7755-4e2c-b57f-5eab32c6a7cc.png">
This seems to be related to authors/affiliations scheme changes since the template file did not change.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-10-31T22:07:57Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 3125,
"state": "closed",
"title": "Affiliation header/label is \"empty\" thus no longer displayed in v1.2",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3125"
} |
The integration with RStudio is good for people working with R, but I think an Integration with DataSpell (the Pycharm-like IDE) could benefits to Python users as well.
What do you think? | {
"assignee": null,
"comments": 3,
"created_at": "2022-10-31T19:01:12Z",
"creator": "slimhk45",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3124,
"state": "open",
"title": "Is a plugin for Jetbrains DataSpell planned?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3124"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3088
<div type='discussions-op-text'>
<sup>Originally posted by **kris-brown** October 28, 2022</sup>
Hi, I have a global `_quarto.yml` with a `date: last-modified` line which applies to all the `.qmd` files in my project.
I then have a listing in my project:
```
listing:
categories: true
type: table
fields: [title, categories, date]
```
But the `date` field is rendered empty unless I explicitly put `date: last-modified` in the corresponding files. Is there anything I can do such that the listing defaults to the global `yml` file when a field isn't found?
</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-10-31T14:48:03Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3121,
"state": "closed",
"title": "Listing field not inherited from global _quarto.yml",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3121"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3031
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** October 25, 2022</sup>
Hi,
a lot of time we have great quarto sites, with very long pages.
In these cases I am missing a back-to-top button, as the one we have in [Material for MkDocs](https://squidfunk.github.io/mkdocs-material/setup/setting-up-versioning/#setting-a-default-version).
if anyone from the core dev group finds it interesting, this is a feature proposal.
Thank you
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-31T13:38:39Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3120,
"state": "closed",
"title": "[Feature proposal]: back-to-top button, for HTML output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3120"
} |
### Bug description
In my experience the image resizing only works if there is at least one additional item on the same slide, this can be text, note, or additional image. Please see below full qmd for the example.
I use `knitr::include_graphics` to include the images. Example of code would be:
```{r}
#| label: fig-autumn1
#| fig-cap: Autumn<br />Krzysztof Popławski, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons
#| out-width: 10%
url1 <- "https://upload.wikimedia.org/wikipedia/commons/b/bc/Park_%C5%9Arodula%2C_Sosnowiec_-_01.jpg"
knitr::include_graphics(url1)
```
## Session info
```
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.2 RC (2022-10-24 r83173)
os macOS Ventura 13.0
system aarch64, darwin21.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Zurich
date 2022-10-31
rstudio 2022.07.2+576 Spotted Wakerobin (desktop)
pandoc 2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.1)
evaluate 0.17 2022-10-07 [1] CRAN (R 4.2.1)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
rmarkdown 2.17 2022-10-07 [1] CRAN (R 4.2.1)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
xfun 0.34 2022-10-18 [1] CRAN (R 4.2.1)
yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.1)
[1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
```
## Copy of the `qmd` Document
```
---
title: "Image Resize"
format: revealjs
editor: visual
---
## Image resize (single) -- doesn't work
```{r}
url1 <- "https://upload.wikimedia.org/wikipedia/commons/b/bc/Park_%C5%9Arodula%2C_Sosnowiec_-_01.jpg"
```
```{r}
#| label: fig-autumn1
#| fig-cap: Autumn<br />Krzysztof Popławski, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons
#| out-width: 10%
knitr::include_graphics(url1)
```
## Image resize (single, with aside) -- works
```{r}
#| label: fig-autumn2
#| fig-cap: Autumn
#| out-width: 10%
knitr::include_graphics(url1)
```
::: aside
Krzysztof Popławski, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons
:::
## Image resize (multiple) -- works
```{r}
#| label: fig-autumn3
#| fig-cap: Autumn<br />Krzysztof Popławski, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons
#| out-width: 10%
knitr::include_graphics(url1)
```
```{r}
#| label: fig-autumn4
#| fig-cap: Autumn<br />Krzysztof Popławski, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons
#| out-width: 25%
knitr::include_graphics(url1)
```
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-10-31T10:27:22Z",
"creator": "ivanek",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3117,
"state": "closed",
"title": "Presentation (revealjs) -- Image resize only works if there is additional item on the same slide",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3117"
} |
### Bug description
When you add [custom appendix sections](https://quarto.org/docs/authoring/appendices.html#custom-appendix-sections) to a post, they are included in the table of contents. I believe this is a bug, as other non-custom sections such as "Citation" are not.
You can see this behaviour in this [blog post](https://blog.djnavarro.net/posts/2022-10-18_arrow-flight/#acknowledgements). The custom "Acknowledgements" section can be seen in the table of contents, but the other sections provided by Quarto are not. The behaviour should be consistent whether an appendix section is custom or not.
As a default leaving appendix entries out of the table of contents makes sense for things like blog posts. But it might be nice to give users control of whether appendix sections are included in the table of contents (e.g., with an `include_appendix` YAML option under `toc`).
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-30T20:19:01Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3113,
"state": "closed",
"title": "Custom appendix sections appear in table of contents",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3113"
} |
### Bug description
When you add [custom appendix sections](https://quarto.org/docs/authoring/appendices.html#custom-appendix-sections) to a post, the headings for these sections are not given an anchor. I believe this is a bug, as other non-custom sections such as citation are given an anchor.
You can see this behaviour in this [blog post](https://blog.djnavarro.net/posts/2022-04-20_porting-to-quarto/#footnotes-1). The sections provided by Quarto have anchors, but the custom "Last updated" and "Details" sections do not. The difference is that the headings for the former section have the `anchored` class, but the latter do not.
Adding the `anchored` class manually while creating an appendix section does not work well either, as the anchor gets put at the end of the section, rather than beside the heading.
```md
## Acknowledgments {.appendix .anchored}
I am grateful for the insightful comments offered by the anonymous peer reviewers at Books & Texts. The generosity and expertise of one and all have improved this study in innumerable ways and saved me from many errors; those that inevitably remain are entirely my own responsibility.
```
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-10-30T20:06:15Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3112,
"state": "closed",
"title": "Custom appendix sections are not anchored",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3112"
} |
### Bug description
I have the input below:
- if I use markdown headings, the slide is not readable
- if I use html headins, it's all ok
I think quarto should manage also the first kind of syntax.
I'm using quarto 1.2.251.
Distributor ID: Debian
Description: Pengwin
Release: 11
Codename: bullseye
```
---
title: "Hello world"
format:
revealjs:
slide-number: true
preview-links: auto
theme: [dark]
navigation-mode: vertical
center-title-slide: false
chalkboard: true
---
# Using Markdown headings
:::: {.columns}
::: {.column width="50%"}
## Colonna 1
:::
::: {.column width="50%"}
## Colonna 2
:::
::::
# Using HTML headings
:::: {.columns}
::: {.column width="50%"}
<h2>Colonna 1</h2>
:::
::: {.column width="50%"}
<h2>Colonna 2</h2>
:::
::::
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-10-30T10:49:49Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3111,
"state": "closed",
"title": "revealjs vertical slides: columns settings does not work well",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3111"
} |
### Bug description
Quarto currently doesn't support custom giscus themes, and instead restricts you to the prebuilt themes. If you input something other than those themes, e.g.:
```yaml
comments:
giscus:
theme: https://giscus.app/themes/custom_example.css
```
You get the following error:
```
Key theme has value https://giscus.app/themes/custom_example.css, which must be one of: `light`, `light_high_contrast`, `light_protanopia`, `dark`, `dark_high_contrast`, `dark_protanopia`, `dark_dimmed`, `transparent_dark`, `preferred_color_scheme`
```
giscus [supports custom themes](https://github.com/giscus/giscus/blob/main/ADVANCED-USAGE.md#data-theme) by supplying a URL to a CSS file as the value for the `data-theme` attribute, and it would be nice if Quarto supported this too.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-10-30T01:11:06Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "v1.3",
"number": 3105,
"state": "closed",
"title": "Custom giscus themes not supported",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3105"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3091
<div type='discussions-op-text'>
<sup>Originally posted by **sje30** October 28, 2022</sup>
Using quarto 1.1.251 with the following file:
````
---
title: "test of julia"
author: "SJE"
engine: jupyter
execute:
echo: true
format:
beamer:
keep-tex: true
monofont: "JuliaMono"
---
## Test slide
```{julia}
println(typeof(ones(3,2)))
```
````
generates the following output
<img width="592" alt="Screenshot 2022-10-28 at 16 56 15" src="https://user-images.githubusercontent.com/1095067/198680965-0007c6af-7674-404c-a9c3-af4d5dfa3100.png">
Here is the relevant .tex chunk
```
\begin{verbatim}
Matrix{
\end{verbatim}
\begin{verbatim}
Float64}
\end{verbatim}
```
whereas it should read `Matrix{Float64}`
</div> | {
"assignee": null,
"comments": 4,
"created_at": "2022-10-28T16:07:23Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3093,
"state": "closed",
"title": "Broken output from a Julia chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3093"
} |
Referring images from parent folder can not be shown correctly in `html` format, see demo code below:
````qmd
---
format: html
---
```{r}
#| echo: false
#| include: false
# generate a image
require(ggplot2)
qplot(1)
ggsave("../img.png")
```
````
I understand that the `html` can not use the resource not inside the working folder, but should we include these resources when rendering to `html` in a smart way?
| {
"assignee": null,
"comments": 1,
"created_at": "2022-10-28T12:06:08Z",
"creator": "mingsu",
"is_pull_request": false,
"labels": [
"wontfix"
],
"locked": false,
"milestone": null,
"number": 3086,
"state": "closed",
"title": "Image from parent folder not shown in `html` format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3086"
} |
### Bug description
When tables get rendered without a `colgroup` element (so whenever columns do not get a specific size), the border at the top of the table doesn't show. For example, in a new website with this `index.qmd`:
``` md
---
title: "Test"
---
| a | a | a |
| - | - | - |
| a | a | a |
| aaaaaaaaa | aaaa | aaaaaaaaaaa |
| - | - | --- |
| aaaaaaaaaaaaa | aaaaaaaaaaaa | aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa |
| aaaaaaaaa | aaaa | aaaaaaaaaaa |
| - | - | --- |
| aaaaaaaaaaaaa | aaaaaaaaaaaaaaaa | aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa |
```
only the third table's top border is rendered. This is because the top border CSS rule is defined as `.table>:not(:first-child)` and the two first tables do not have the `colgroup` element (I think this is Pandoc?).
I'm using Quarto v1.2.242.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-10-28T10:49:29Z",
"creator": "tomvaneyck",
"is_pull_request": false,
"labels": [
"bug",
"tables"
],
"locked": false,
"milestone": "v1.3",
"number": 3084,
"state": "closed",
"title": "Top border table does not get rendered without `colgroup`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3084"
} |
### Bug description
I can render the following script on its own just fine:
````
```{python}
from bokeh.io import output_notebook, show
from bokeh.layouts import gridplot
from bokeh.plotting import figure
output_notebook()
x = list(range(11))
y0 = x
y1 = [10-xx for xx in x]
y2 = [abs(xx-5) for xx in x]
# create a new plot
s1 = figure(width=250, height=250, title=None)
s1.circle(x, y0, size=10, color="navy", alpha=0.5)
# create a new plot and share both ranges
s2 = figure(width=250, height=250, x_range=s1.x_range, y_range=s1.y_range, title=None)
s2.triangle(x, y1, size=10, color="firebrick", alpha=0.5)
# create a new plot and share only one range
s3 = figure(width=250, height=250, x_range=s1.x_range, title=None)
s3.square(x, y2, size=10, color="olive", alpha=0.5)
p = gridplot([[s1, s2, s3]], toolbar_location=None)
# show the results
show(p)
```
````
However, adding an empty R cell in front rises a NameError:
````
```{r}
```
````
Gives :
```
Erreur dans py_call_impl(callable, dots$args, dots$keywords) :
NameError: name 'figure' is not defined
Appels : .main ... py_capture_output -> force -> <Anonymous> -> py_call_impl
```
---
RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_4_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
---
ProductName: macOS
ProductVersion: 12.4
BuildVersion: 21F79
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 27,
"created_at": "2022-10-28T09:53:56Z",
"creator": "katossky",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3083,
"state": "closed",
"title": "NameError when mixing R and Python cells",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3083"
} |
### Bug description
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-28T05:24:23Z",
"creator": "Achuan-2",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3081,
"state": "closed",
"title": "code content auto breakline",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3081"
} |
### Bug description
biblatex
citeproc
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-28T03:56:40Z",
"creator": "Achuan-2",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3080,
"state": "closed",
"title": "biblatex dont't render with csl style",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3080"
} |
Trying to make my Quarto website 508 compliant, but I'm not seeing any way to add alternate text to the image on my "About" page. Any suggestions? | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-10-27T17:44:27Z",
"creator": "ameliaritger",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3383,
"state": "closed",
"title": "No option for adding alt text to About Pages images",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3383"
} |
@cscheid per our conversation -
When working with custom ejs formats for content listings I find myself wanting to add additional metadata. However I am limited to either using the default metadata available from auto content listings (ref: https://quarto.org/docs/websites/website-listings.html#listing-fields) OR defining my own custom metadata that's passed into the ejs format (ref: https://quarto.org/docs/websites/website-listings.html#listing-fields). However if I use the latter, I lose access to the default metadata from the former.
Would like to be able to add additional metadata to content listings using a format like:
```
listing:
- id: sample
template: custom.ejs
contents:
- auto: content-folder
custom-field: "custom metadata I want to add"
``` | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-10-27T16:48:46Z",
"creator": "kmasiello",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 3071,
"state": "closed",
"title": "Website listings - supplement auto content with custom metadata",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3071"
} |
### Bug description
Hello,
I mostly edit in VScode but occasionally switch to RStudio to use the visual editor for idiosyncratic reasons. I've noticed when subsequently switching back to VScode that my line numbering has been changed around inline math. For example, if I originally had
```
The equation is
$$
Y = ax + b.
$$
That is a line.
```
This is then converted to something like
```
The equation is $$
Y = ax + b.
$$ That is a line.
```
which creates problems down the line for code coloring and folding.
Running RStudio 2022.07.0 Build 548 on macOS Ventura (but also experienced this issue before upgrading to Ventura).
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-10-27T15:22:10Z",
"creator": "halidaee",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3069,
"state": "closed",
"title": "Opening .qmd in RStudio visual editor changes line numbering (especially for display style equations)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3069"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3064
<div type='discussions-op-text'>
<sup>Originally posted by **apreshill** October 27, 2022</sup>
Hello 👋
I need to use a local font file in a Quarto-rendered revealjs HTML presentation. I can get the font to render locally, but not when deployed to GitHub pages. Here is a reprex repo:
https://github.com/apreshill/reveal-fonts-reprex
The rendered deck: https://apreshill.github.io/reveal-fonts-reprex/
Note that I have `embed-resources: true` in the YAML: https://github.com/apreshill/reveal-fonts-reprex/blob/f2461431caa84681d45bbb8b06e387ee04b92918/index.qmd#L3 (it didn't work with this set to `true` or `false` though)
I get this error rendering locally after adding that to my YAML:
> `pandoc: /fonts/bodoni-moda-v7-latin-regular.woff2: openBinaryFile: does not exist (No such file or directory)`
I've tried all manner of file path combinations here since this looks like pandoc is struggling to find the file based on my file path, but I'm getting nowhere.
Here is what it looks like locally (with the custom font working fine):
<img width="1501" alt="Screen Shot 2022-10-27 at 2 55 06 PM" src="https://user-images.githubusercontent.com/12160301/198290155-b3c8af6d-76ed-4bbe-954e-d12d9f58df3e.png">
Any pointers? Thanks.</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-27T14:54:48Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3068,
"state": "closed",
"title": "Using a custom local font file with revealjs presentations",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3068"
} |
### Bug description
# Quarto-mermaid-docx
I'm trying to use mermaid to produce a diagram in html, pdf and docx output. When I use Ctrl Shift B / Render All Formats, I get the following error:
`
ERROR: TypeError: error sending request for url (http://localhost:9222/json/list): error trying to connect: tcp connect error: No connection could be made because the target machine actively refused it. (os error 10061)
`
Regarding the output format:
- If I remove docx from the output in the YML file, the book renders correctly in pdf and html, when I use render all formats.
- If I remove pdf from the output in the YML file, the book renders correctly in docx and html, when I use render all formats.
- If I select rendering to MS Word only, the book renders correctly.
- If I select rendering to pdf only, the book renders correctly.
Regarding mermaid:
- If I remove the mermaid diagram, the book renders to all output formats without errors.
- If I wrap the mermaid code in `::: {.content-visible unless-format="docx"} :::` or similar, I still get the error when I try to render to all formats
Version running:
- Quarto 1.2
- "Elsbeth Geranium" Daily (896a0002, 2022-08-02) for Windows
- R version 4.0.5 (2021-03-31) -- "Shake and Throw"
- Platform: x86_64-w64-mingw32/x64 (64-bit)
The obvious solution for me is not to use the Render All Formats option. But it took me way too long to find out, so I thought this may be helpful to know.
index.qmd:
````
# Preface
```{mermaid}
flowchart TB
a(1.)
b[2.]
a --> b
```
bla bla bla
````
_quarto.yml:
````
project:
type: book
book:
title: "Mermaid docx pdf test"
chapters:
- index.qmd
format:
html:
theme: cosmo
pdf:
documentclass: scrreprt
docx: default
editor: source
````
Here's a repository, which essentially contains the snippets here:
https://github.com/VMTdeJong/Quarto-mermaid-docx
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 15,
"created_at": "2022-10-27T13:34:58Z",
"creator": "VMTdeJong",
"is_pull_request": false,
"labels": [
"bug",
"mermaid",
"puppeteer"
],
"locked": false,
"milestone": "v1.3",
"number": 3066,
"state": "closed",
"title": "Cannot render mermaid to docx and pdf simultaneously",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3066"
} |
786: comment_chars <- knitr_engine_comment_chars[[engine]] %||% "#"
787: comment_start
^
Calls: .main -> source
ͣ�� | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-27T11:14:04Z",
"creator": "zhangqianfu",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3065,
"state": "closed",
"title": "new error happened when compile qmd file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3065"
} |
I hope you don't mind me posting them in this thread, but I found another "quirk" relating to `lang:` setting in dates that have names of months (not just for books). I'm on windows, so maybe it's OS specific? Here's a MWE:
```markdown
---
title: "MWE"
lang: fr-FR
date: last-modified
date-format: "DD MMMM YYYY à HH:mm:ss Z"
---
Here's some text.
```
Rendering this in HTML or PDF will show a date that is not French (note "October" rather than "octobre").
> MWE
> DATE DE PUBLICATION
> 26 October 2022 à 09:59:56 -04:00
>
> Here’s some text.
The workaround is to drop the country from the language, e.g., `lang: fr` -- it's probably another bug with pandoc?
> MWE
> DATE DE PUBLICATION
> 26 octobre 2022 à 10:00:57 -04:00
>
> Here’s some text. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-26T21:22:21Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3059,
"state": "closed",
"title": "Implement fallback logic for loading date locales",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3059"
} |
The following document makes `quarto render --to docx` hang:
````
---
title: "Untitled"
---
```{r include=FALSE}
library(officer)
library(officedown)
library(flextable)
knitr::opts_chunk$set(echo = FALSE)
```
```{r}
#| label: tbl-flextable
#| tbl-cap: First Flextable
flextable::flextable(mtcars[1:4, 1:4])
```
```{r}
#| label: tbl-flextable2
#| tbl-cap: Second Flextable
flextable::flextable(mtcars[1:4, 1:4])
```
```` | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-10-26T19:19:43Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 3057,
"state": "closed",
"title": ".docx rendering with flextable hangs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3057"
} |
### Bug description
The `quarto inspect` command does not include images in its resource list, which forces manual resource addition when publishing.
Given the Quarto document:
```markdown
---
format: revealjs
---
# Presentation {background-image="logo.svg" background-opacity="0.2"}
```
Any two images can be used for this example, just make sure you use distinct images for the background and the inline image.
The `quarto inspect` command returns an empty set of resources:
```bash
quarto inspect | jq '.files.resources'
# => []
```
This causes problems when publishing the content, as the images are not included in the deployed bundle by default.
From RStudio, part of the problem is avoided because `rmarkdown::find_external_resources` reports the inline image.
```r
rmarkdown::find_external_resources("index.qmd")
# => path explicit web
# => 1 bcorps-logo.svg FALSE TRUE
```
The `quarto::quarto_publish_doc` function merges the Quarto `resources` from `quarto inspect` (though not the `files.resources`) with the results from `rmarkdown::find_external_resources`.
https://github.com/quarto-dev/quarto-r/blob/146bb4ed542ef5743cd182464d17919bcfb5b0eb/R/publish.R#L49
https://github.com/quarto-dev/quarto-r/blob/146bb4ed542ef5743cd182464d17919bcfb5b0eb/R/publish.R#L104-L109
I'm not sure if the RStudio publishing flow is different from the `quarto_publish_doc` implementation.
Quarto source resources should be identified when publishing through some combination of these pieces. Currently, the `logo.svg` used as a slide background is not identified.
Quarto: 1.2.242
RStudio: 2022.12.0-daily+286
rmarkdown: 2.14
macOS: Monterey (12.6)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-10-26T17:23:07Z",
"creator": "aronatkins",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3053,
"state": "open",
"title": "Image resources not enumerated in inspect output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3053"
} |
### Bug description
Using the latest Quarto with version with latest tools on Windows 11, VSCode:
```sh
Quarto: 1.2.242
Tool Status Installed Latest
chromium Up to date 869685 869685
tinytex Up to date v2022.10 v2022.10
```
In _quarto.yml:
```
project:
title: "test"
output-dir: .output
author: Jonathan Johnson
format:
revealjs:
theme: [dark, custom.scss]
highlight-style: dracula # arrow
preview-links: auto
code-line-numbers: "false"
transition: convex
chalkboard:
boardmarker-width: 5
code-copy: true
pdf:
toc: true
number-sections: true
colorlinks: true
toc-title: Contents
highlight-style: github
# pdf-engine: wkhtmltopdf
# pdf-engine: xelatex
from: markdown+emoji
execute:
echo: false
```
With this qmd:
```
---
title: "Test of rendering mermaid to pdf"
---
## Binary Tree
```{mermaid}
%%| fig-width: 5.5
%%{init: {'theme':'dark'}}%%
graph TB
A((8))-->B((3))
A-->C((10))
B-->D((1))
B-->E((6))
C-->F((9))
C-->G((14))
E-->H((4))
E-->I((7))
```
```
This renders to the HTML, browser with reveal.js, but not to PDF.
It appears the root error is: "Could not load mf.dll:"
Here is the output with the error:
```sh
quarto preview [redacted path]/pdf-render-error.qmd --to pdf --no-browser --no-watch-inputs
ERROR: Couldn't find open server.
Chrome process error: [1026/111558.776:WARNING:resource_bundle.cc(405)] locale_file_path.empty() for locale
[1026/111558.776:ERROR:resource_bundle.cc(911)] Failed to load C:\Users\jonat\AppData\Local\quarto\chromium\win64-869685\chrome-win\resources.pak
Some features may not be available.
[1026/111558.802:WARNING:headless_browser_main_parts.cc(106)] Cannot create Pref Service with no user data dir.
[1026/111558.803:ERROR:dxva_video_decode_accelerator_win.cc(1406)] DXVAVDA fatal error: Could not load mf.dll: The specified module could not be found. (0x7E)
DevTools listening on ws://127.0.0.1:9222/devtools/browser/50bced1c-1d60-4c43-aadb-f2fe69c062b2
[1026/111558.805:ERROR:gpu_channel_manager.cc(746)] ContextResult::kFatalFailure: Failed to create shared context for virtualization.
[1026/111558.806:ERROR:shared_image_stub.cc(460)] SharedImageStub: unable to create context
[1026/111558.806:ERROR:gpu_channel.cc(449)] GpuChannel: Failed to create SharedImageStub
#
# Fatal error in , line 0
# Failed to deserialize the V8 snapshot blob. This can mean that the snapshot blob file is corrupted or missing.
#
#
#
#FailureMessage Object: 000000B6701FF4B0Backtrace:
IsSandboxedProcess [0x00007FFCE39C0BE2+728514]
IsSandboxedProcess [0x00007FFCE393DA32+191506]
IsSandboxedProcess [0x00007FFCE43BFAD7+11209911]
IsSandboxedProcess [0x00007FFCE3FBE089+7008873]
ovly_debug_event [0x00007FFCE290463F+27991791]
IsSandboxedProcess [0x00007FFCE43BD992+11201394]
IsSandboxedProcess [0x00007FFCE43E55F3+11364307]
IsSandboxedProcess [0x00007FFCE43E5D35+11366165]
RelaunchChromeBrowserWithNewCommandLineIfNeeded [0x00007FFCE5E04179+25911353]
RelaunchChromeBrowserWithNewCommandLineIfNeeded [0x00007FFCE61E7BAD+29989485]
RelaunchChromeBrowserWithNewCommandLineIfNeeded [0x00007FFCE515A5DC+12633244]
RelaunchChromeBrowserWithNewCommandLineIfNeeded [0x00007FFCE51597DC+12629660]
RelaunchChromeBrowserWithNewCommandLineIfNeeded [0x00007FFCE51594A8+12628840]
IsSandboxedProcess [0x00007FFCE4427894+11635316]
IsSandboxedProcess [0x00007FFCE39AB64D+641069]
IsSandboxedProcess [0x00007FFCE39D1860+797248]
BaseThreadInitThunk [0x00007FFD90BC244D+29]
RtlUserThreadStart [0x00007FFD9238DFB8+40]
```
In exploring the notion that `mf.dll` might be missing the research found that `mf.dll` is related to Media Foundation features in Windows 11. I verified that the media player feature is enabled and installed in this Windows machine and ran "DISM.exe /Online /Cleanup-image /Scanhealth" to verify the integrity of the Windows 11 installation. The C:\Windows\System32\mf.dll file is present and appears to be the expected size. All appears healthy and normal. Both the Windows Player and legacy player are present and functional.
Then in reading the docs more, quarto says that the chromium engine/plugin is used to render the output. The tools list says its the latest, but I suspected the installation was corrupt and the tool list just verifies the version but not the integrity of its installation.
I uninstalled the chromium tool using `quarto tools uninstall chromium` then reinstalled with `quarto tools install chromium`.
The pdf rendering with mermaid worked after that.
Suggestions:
1. The "quarto tool list" or another command could perform a integrity check.
2. The documentation for PDF rendering (there are too many different pages on PDF rendering) should suggest uninstalling and reinstalling if there is a problem.
3.
(Also, in the [docs](https://quarto.org/docs/output-formats/pdf-engine.html#quarto-pdf-engine) I think all the commands that read `quarto install [x]` should instead read `quarto tools install [x]`.) | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-26T16:59:19Z",
"creator": "javajon",
"is_pull_request": false,
"labels": [
"windows",
"puppeteer"
],
"locked": false,
"milestone": "Future",
"number": 3052,
"state": "open",
"title": "Hang then error when rending Mermaid graph to PDF ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3052"
} |
### Bug description
When previewing a website in Firefox using `quarto preview`, only the homepage loads; whenever clicking any other link in both the navbar or sidebar, the homepage reloads. Quarto gives the following output on clicking a link (but only sometimes):
```
GET: /about.html
WARNING: connection closed before message completed
GET: /
```
while Firefox shows the following in the developer tools:
I'm using Quarto v1.2.242 and see the result both running on Windows 11 in Powershell and in WSLv1.
### Reproducing
1. Create a new website using `quarto create project website`.
2. Execute `quarto preview`.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-10-26T12:44:17Z",
"creator": "tomvaneyck",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 3045,
"state": "closed",
"title": "Quarto preview only loading homepage in Firefox",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3045"
} |
This is on us: https://github.com/rstudio/gt/issues/1085 | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-10-25T20:41:29Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"tables"
],
"locked": false,
"milestone": null,
"number": 3038,
"state": "closed",
"title": "Missing selectors for gt style override",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3038"
} |
### Bug description
I'm working in Quarto and needing to convert to Word for the sake of my co-authors. I'm getting a problem with the way a display equation containing a matrix is rendering.
[MatrixTest.qmd.txt](https://github.com/quarto-dev/quarto-cli/files/9863877/MatrixTest.qmd.txt)
In my Markdown document I have
```md
$$ \begin{array}{ccccc}
\end{array} $$
```
In RStudio, it is working fine. However, when I try to render it as word, instead of rendering the equation, I get the raw latex commands (i.e, everything between the dollars).
I'm using RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
I'm attaching a small example that breaks.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-10-25T20:40:01Z",
"creator": "ralmond",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3037,
"state": "closed",
"title": "Latex Matrix not rendering in Word",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3037"
} |
### Bug description
There was a change between quarto 1.1.251 and 1.2.242 such that rendering html fails with SELinux enabled.
With a trivial hello world test.qmd file I get the following with 1.2.242:
```
$ quarto render test.qmd
tcc: error: mprotect failed: did you mean to configure --with-selinux?
```
With 1.1.151 is works fine. Disabling SELinux allows quarto 1.2.242 to work as expected. Generating other formats
like jats or tex does not hit this issue.
This happens with both Fedora 36 (in a container) and RHEL 9.0.
The SELinux violation is a deno process attempting execheap access. The default SELinux policy is to not permit this. From my understanding execheap access is to allow heap memory to be both writable and executable. This in turn allows a greater attack surface.
Here's what the SELinux Alert Browser reports:
```
The deno application attempted to change the access protection of memory on the
heap (e.g., allocated using malloc). This is a potential security problem.
Applications should not be doing this. Applications are sometimes coded
incorrectly and request this permission. The SELinux Memory Protection Tests
web page explains how to remove this requirement. If deno does not work and you
need it to work, you can configure SELinux temporarily to allow this access
until the application is fixed. Please file a bug report against this package.
If you do not think /home/castedo/shr/quarto-1.2.242/bin/tools/deno-x86_64-unknown-linux-gnu/deno
should need to map heap memory that is both writable and executable.
you need to report a bug. This is a potentially dangerous access.
Contact your security administrator and report this issue.
```
Seems strange that authoring software to generate HTML from markdown needs to be doing something exotic like writing machine code to the heap and then have it executed. Version 1.1.251 didn't need to do this to generate HTML. Seems far less annoying to stop doing this, especially if a server process is having quarto generate static HTML files.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-25T17:54:14Z",
"creator": "castedo",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3036,
"state": "closed",
"title": "SELinux execheap access violation generating HTML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3036"
} |
We're scraping the latest GH release version from this repo automatically for some internal automation. Is it planned to keep it up-to-date?
The latest Quarto release is 1.2.242 since some days but this repo is still sitting at 1.1.251 :) | {
"assignee": null,
"comments": 6,
"created_at": "2022-10-25T16:05:40Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3032,
"state": "closed",
"title": "Latest GitHub release",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3032"
} |
### Bug description
Sorry for the weird issue title.
If I try to add `lines()` or `points()` to a plot when looping in a `data.table` (using argument `by`), only the last "by call" shows up in the output figure. E.g. if the following code is rendered in a simple quarto document, only 1 line (lab == 'd') is showing instead of 4 lines:
````qmd
---
format: pdf
---
```{r}
#| label: fig-example
#| fig-cap: "Only showing 1 line"
#| fig-asp: 1
#| fig-width: 3
library(data.table, quietly = TRUE)
Nlab <- 4
dt <- data.table(
lab = rep(letters[1:Nlab], each = 2),
x = runif(Nlab * 2, -200, 100), y = runif(Nlab * 2, -200, 100))
plot(1, type = 'n', xlim = c(-200, 100), ylim = c(-200, 100))
invisible(dt[, {
points(x, y, pch = 20)
lines(x, y)
}, by = lab])
dt
```
````
My quarto version is 1.2.242.
I'm running R in a terminal, not in R Studio, on Debian 11.
My `sessionInfo()`:
```r
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Progress Linux 6.99 (fuchur-backports)
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.14.2 colorout_1.2-2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 ps_1.7.1 RhpcBLASctl_0.21-247.1 digest_0.6.29 later_1.3.0 R6_2.5.1 jsonlite_1.8.0 evaluate_0.16 rlang_1.0.4
[10] cli_3.3.0 rstudioapi_0.14 rmarkdown_2.16 tools_4.2.1 glue_1.6.2 yaml_2.3.5 xfun_0.32 fastmap_1.1.0 compiler_4.2.1
[19] processx_3.7.0 htmltools_0.5.3 knitr_1.40 quarto_1.2
```
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 2,
"created_at": "2022-10-25T15:07:55Z",
"creator": "ChHaeni",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3029,
"state": "closed",
"title": "'by'-looping over data.table: only last 'by'-call to points()/lines() shows in output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3029"
} |
### Bug description
Opening a Quarto website (or book) from a local drive in a browser (file:///) blocks search from working due to CORS policies in modern browsers (tested on Firefox 105 & Edge 106).
Error message from Firefox:
Cross-Origin Request Blocked: The Same Origin Policy disallows reading the remote resource at file:///../search.json (Reason: CORS request not http)
Error message from Edge:
Access to fetch at 'file:///.../search.json' from origin 'null' has been blocked by CORS policy: Cross origin requests are only supported for protocol schemes: http, data, isolated-app, chrome-extension, chrome-untrusted, https, edge.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2022-10-25T14:51:14Z",
"creator": "GthSd",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3028,
"state": "closed",
"title": "Search blocked for Quarto website not on webserver",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3028"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3023
<div type='discussions-op-text'>
<sup>Originally posted by **mcanouil** October 25, 2022</sup>
I don't know if it's really a bug or some kind of misconfiguration, but for both Twitter and OpenGraph cards, the image is not found or none are defined.
See for example <https://twitter.com/MickaelCanouil/status/1584884666913345536>.
EDIT: the search mechanism to find a preview image (or the propagation of it) seems to take longer than it usually does compared to when the image is set.
Also, there might be something wrong (or not clear at least) in the documentation: <https://quarto.org/docs/websites/website-tools.html#twitter-cards>.
| Option | Description |
|:-------|:------------|
| image | The path to a preview image for this content. By default, Quarto will use the image `value` from the `site:` metadata. If you provide an image, you may also optionally provide an `image-width` and `image-height` to improve the appearance of your Twitter Card. If image is not provided, Quarto will automatically attempt to locate a preview `image`. For more information, see Preview Images. |
Here, the description talks about `site:`, is it really this option or is it `website:`?
It's a bit confusing because there is a `site:` option listed in the same table.
| Option | Description |
|:-------|:------------|
|site | @username of website. Note that strings with special characters such as @ must be quoted in yaml.|
If it's indeed `website:` and not `site:`, then the default image that should be taken for Twitter and OpenGraph cards should be the one in <https://github.com/quarto-dev/quarto-web/blob/4a665d2e5082a7e80a3bb566b3924673f1de7f45/_quarto.yml#L9-L11>, but that's not the case.
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-25T13:03:54Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.3",
"number": 3024,
"state": "closed",
"title": "Issues with social images on quarto.org 🤔 (maybe not specific though)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3024"
} |
### Bug description
Map with `ipyleaflet` shows in Jupyter notebook, but not showing on the final rendered slides.
Os: Ubuntu 22.04
VScode: 1.72.2
Quarto: 1.1.251
Quarto VScode extension: v1.51.0
[leaflet_map.zip](https://github.com/quarto-dev/quarto-cli/files/9856773/leaflet_map.zip)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-25T03:00:34Z",
"creator": "rleyvasal",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3019,
"state": "closed",
"title": "`ipyleaflet` not showing map on rendered quarto slides VScode + Jupyter + Python + Revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3019"
} |
### Bug description
Os: Ubuntu 22.04
VScode: 1.72.2
Quarto: 1.1.251
Quarto VScode extension: v1.51.0
I am following the example in the [quarto docs](https://quarto.org/docs/interactive/ojs/) to bring a pandas dataframe to OJS in Jupyter notebook but I get error `'ojs_define' is not defined`
[ojs_jupyter.zip](https://github.com/quarto-dev/quarto-cli/files/9856642/ojs_jupyter.zip)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-25T02:29:55Z",
"creator": "rleyvasal",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3018,
"state": "open",
"title": "`ojs_define()` in python jupyter notebook error `'ojs_define' is not defined` VScode + Jupyter + Python + Revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3018"
} |
### Bug description
Bug description: Ipywidgets work in jupyter notebook to change a plot, but when rendering to Revealjs slides the interactivity of the sliders does not work on the plot.
Os: Ubuntu 22.04
VScode: 1.72.2
Quarto: 1.1.251
Quarto VScode extension: v1.50.0
# Screenshot of Ipywidget in browser (slides move but plot does not change)
[Ipywidgets_jupyter.zip](https://github.com/quarto-dev/quarto-cli/files/9855499/Ipywidgets_jupyter.zip)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-10-24T21:40:08Z",
"creator": "rleyvasal",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3016,
"state": "closed",
"title": "Ipywidgets interactive sliders do change plot in rendered slides VScode + Jupyter + Python + Revealjs ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3016"
} |
### Bug description
Using unicode letters and rendering to pdf results in the letters bein omitted (on manjaro linux, vscode). Setting
```yaml
mainfont: Times New Roman
```
lets me render unicode in the main text flow, but not in code blocks. Also this option results in an error when run on my system because the font is not installed. This is not the best UX. This should just work without user interaction.
See this example:
````
---
title: "test"
jupyter: julia-1.8
---
```{julia}
α=3
```
α is a great constant.
````
------------------------------------------------------------------------------
The output is
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cwickham",
"comments": 7,
"created_at": "2022-10-24T20:30:27Z",
"creator": "peteole",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 3013,
"state": "open",
"title": "Greek unicode letters not rendered in pdf output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3013"
} |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.