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From https://community.rstudio.com/t/quarto-errors-out-when-calling-dt-inline/159894/3
This works in R Mardown
````markdown
---
title: "Test"
output: html_document
---
```{r da-table}
#| echo: false
#| essage: FALSE
atsi.need <- DT::datatable(iris)
```
Under ESSA student groups are identified for Additional Targeted Support and Improvement.
`r atsi.need`
````
This does not in Quarto
````markdown
---
title: "test"
format: html
keep-md: true
---
Works
```{r da-table, echo=FALSE, message=FALSE}
atsi.need <- DT::datatable(iris)
atsi.need
```
but error
Under ESSA student groups are identified for Additional Targeted Support and Improvement.
`r atsi.need`
````
with this error
````
++ Activating rlang global_entrace
++ Setting QUARTO_PYTHON
processing file: test2.qmd
|...........................................................| 100% Quitting from lines 12-15 (test2.qmd)
Error in `rep_len()`:
! impossible de répliquer NULL vers une longueur non nulle
Backtrace:
1. global .main()
2. execute(...)
3. rmarkdown::render(...)
4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
5. knitr:::process_file(text, output)
...
9. knitr:::call_inline(x)
12. knitr:::inline_exec(block)
13. sew(res, inline = TRUE)
14. knitr:::sew.knit_asis(x, options, ...)
15. knitr::knit_meta_add(m, if (missing(options)) "" else options$label)
Message d'avis :
The closing backticks on line 11 ("````") in test2.qmd do not match the opening backticks "```" on line 7. You are recommended to fix either the opening or closing delimiter of the code chunk to use exactly the same numbers of backticks and same level of indentation (or blockquote).
Exécution arrêtée
++ Activating rlang global_entrace
```` | {
"assignee": "cderv",
"comments": 0,
"created_at": "2023-02-17T11:10:51Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4402,
"state": "closed",
"title": "Inserting HTML widgets with knitr inline content is not working the same as in R Markdown",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4402"
} |
From https://community.rstudio.com/t/how-to-fix-the-title-banner-to-the-top-of-page/158650/2
> I am looking for a solution to fix the title banner to the top of the rendered html page, while the rest of the page remains scrollable.
Currently we have no option for that. This issue track the idea of adding one. Upvote if interested. 👍 | {
"assignee": null,
"comments": 3,
"created_at": "2023-02-17T09:26:41Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 4401,
"state": "open",
"title": "[FR] Allow a configuration to make the navbar sticky in Quarto website",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4401"
} |
I've been using Quarto for my personal page and blog for a few months now, but starting a few weeks back I haven't been able to access the internal preview feature from VS code. When I click render, the terminal executes the command
`quarto preview /Users/shio
nfukuzawa/shifubear.github.io/posts/lglar-ch3/index.qmd --no-browser --no-watch-inputs`
Then after generating the preview, prints out this message and I get no response after
`Browse at <jupyterhub-server-url>/user/myemail/proxy/4560/posts/lglar-ch3/index.html`
I'm not sure if there is not supposed to be a jupyterhub-server-url here, and haven't been able to find anyone having similar issues. I've tried uninstalling and reinstalling Quarto but it doesn't seem to help.
Any suggestions on how to fix this? | {
"assignee": null,
"comments": 5,
"created_at": "2023-02-17T01:27:56Z",
"creator": "shifubear",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4408,
"state": "closed",
"title": "VS Code internal preview not working anymore",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4408"
} |
### Bug description
When using the multi-format feature, formats that resolve to the same file extension aren't distinguished. For example, for a file called `test.qmd` with both `html` and `revealjs` formats specified, the RevealJS link points to `test.html` and gets the HTML page, not the revealJS presentation.
The same problem arises with `pdf` and `beamer` formats.
An example:
````
---
title: Multi format example
format:
html: default
revealjs: default
---
## Getting up
- Turn off alarm
- Get out of bed
## Going to sleep
- Get in bed
- Count sheep
````
Dev Quarto, Mac OS, RStudio Version 2023.03.0-daily+302 (2023.03.0-daily+302)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-02-16T23:38:13Z",
"creator": "cwickham",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4398,
"state": "closed",
"title": "Multi-format links don't distinguish formats with same extension",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4398"
} |
I haven't been able to get this working. Here's a minimal repo: [https://github.com/andrewpbray/publish-profile](https://github.com/andrewpbray/publish-profile).
`quarto render --profile alternate` works just fine and `quarto publish` works just fine (it goes to `gh-pages`). But when I run `quarto publish --profile alternate` I get `ERROR: Publishing source 'alternate' not found`.
Is there something I'm missing with the syntax?
I have been able to publish profiles using environmental variables (see [this workflow](https://github.com/stat20/course-materials/blob/main/.github/workflows/publish-partial.yml)) but doing it via an option on `quarto publish` is where I get hung up.
_Originally posted by @andrewpbray in https://github.com/quarto-dev/quarto-cli/discussions/4076#discussioncomment-5000552_
It is documented
````bash
$ quarto publish --help
Usage: quarto publish [provider] [path]
Version: 99.9.9
Description:
Publish a document or project. Available providers include:
- Quarto Pub (quarto-pub)
- GitHub Pages (gh-pages)
- RStudio Connect (connect)
- Netlify (netlify)
Accounts are configured interactively during publishing.
Manage/remove accounts with: quarto publish accounts
Options:
-h, --help - Show this help.
--id <id> - Identifier of content to publish
--server <server> - Server to publish to
--token <token> - Access token for publising provider
--no-render - Do not render before publishing.
--no-prompt - Do not prompt to confirm publishing destination
--no-browser - Do not open a browser to the site after publishing
--log <level> - Path to log file
--log-level <level> - Log level (info, warning, error, critical)
--log-format <format> - Log format (plain, json-stream)
--quiet - Suppress console output.
--profile - Active project profile(s)
````
But not working somehow it seems. | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2023-02-16T21:47:46Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"publishing"
],
"locked": false,
"milestone": "v1.3",
"number": 4396,
"state": "closed",
"title": "`quarto publish --profile` is not working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4396"
} |
> Yes, while running quarto, it kept giving the message that deno upgrade is available
Oof, that's super annoying, I'm sorry. We're supposed to have a command-line flag to disable that warning, but clearly it's not working for you. @cderv do you see this upgrade nag on windows?
_Originally posted by @cscheid in https://github.com/quarto-dev/quarto-cli/issues/4388#issuecomment-1433511448_
## Context
https://deno.com/blog/v1.27#upgrade-checker
> We took special care to ensure that these checks don't impact the performance of your applications - they only happen in the background at most once a day. This feature can be disabled entirely by setting the environment variable: DENO_NO_UPDATE_CHECK=1
Somehow it does not seem to work on Windows
| {
"assignee": "cderv",
"comments": 5,
"created_at": "2023-02-16T21:26:56Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"windows"
],
"locked": false,
"milestone": "v1.4",
"number": 4394,
"state": "closed",
"title": "Ensure deno upgrade warning deactivation works on Windows ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4394"
} |
### Bug description
When wide tibbles are displayed in revealjs slides, they wrap onto a second line.
```` md
---
title: "Untitled"
format: revealjs
editor: visual
---
## A dataset
```{r}
library(dplyr)
bind_cols(mtcars, mtcars) |> as_tibble()
```
````
In the console, it looks like this:
In the rendered slide, it looks like this:
I'd expect the output to show one row per line.
**Software**:
RStudio: Version 2022.12.0+353 (2022.12.0+353)
macOS: 13.1 (22C65)
Quarto: 1.2.335
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2023-02-16T19:39:56Z",
"creator": "Aariq",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4392,
"state": "closed",
"title": "tibble width doesn't match display width in revealjs ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4392"
} |
### Bug description
This document renders correctly:
```
---
title: Here is a first title
author: Iam Author
format:
pdf:
mainfont: Latin Modern Roman
sansfont: Latin Modern Roman
#pdf-engine: pdflatex
---
# First section
Here is some body text
```
If I remove the hash in front of `pdf-engine`, so that rendering uses `pdflatex` rather than `xelatex`, the font options are ignored. The two rendered examples are attached.
Not sure if this is a bug, but if not it should be documented. (I looked, but in general had trouble figuring out the font options from the online documentation.)
This is using quarto version 1.3.191 on Ubuntu 22.04, and pdflatex is `pdfTeX 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) kpathsea version 6.3.4/dev`
[pdf-fonts-issue.zip](https://github.com/quarto-dev/quarto-cli/files/10759258/pdf-fonts-issue.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": "cwickham",
"comments": 3,
"created_at": "2023-02-16T18:22:36Z",
"creator": "rmcd1024",
"is_pull_request": false,
"labels": [
"bug",
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4390,
"state": "closed",
"title": "Font options don't work with pdflatex",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4390"
} |
### Bug description
Is this a bug or am I doing something incorrect?
quarto version: 1.3.203
Windows 10
deno 1.30.3 (release, x86_64-pc-windows-msvc)
v8 10.9.194.5
typescript 4.9.4
1) Created a new book
```
C:\sw>quarto create-project qbook2 --type book
Creating project at G:\gdac\qbook2:
- Created _quarto.yml
- Created index.qmd
- Created intro.qmd
- Created summary.qmd
- Created references.qmd
- Created cover.png
- Created references.bib
```
2) started local preview without modifications.
```
C:\sw>cd qbook2
C:\sw\qbook2>quarto preview
Preparing to preview
[1/4] index.qmd
[2/4] intro.qmd
[3/4] summary.qmd
[4/4] references.qmd
Watching files for changes
Browse at http://localhost:3286/
GET: /
GET: /intro.html
GET: /intro.html
GET: /summary.html
GET: /intro.html
GET: /intro.html
```
### Desktop Mode: Chapter 1 Introduction heading is displayed properly.
### Mobile Mode: Chapter 1 Introduction heading is displaying its code as a string.
"Preface" and "References as headings display properly but Chapters don't display properly in mobile or responsive mode.
```html
<ol class="breadcrumb">
<li class="breadcrumb-item">
<a href="http://localhost:3286/intro.html"><span class='chapter-number'>1</span> <span class='chapter-title'>Introduction</span></a>
</li>
</ol>
```
### Similar for Chapter 2 in mobile mode.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2023-02-16T16:45:19Z",
"creator": "fortunewalla",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4388,
"state": "closed",
"title": "quarto create-project new book preview breaks chapter heading in mobile responsive mode",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4388"
} |
### Bug description
Setting: Quarto Website using a theme.
Objective: I would like to avoid downloading google fonts via the google api
Idea: Storing the fonts locally and include them via a custom scss file
`_quarto.yml`:
```yml
format:
html:
theme:
light: [flatly, light.scss]
```
`light.scss`:
```css
/* lato-regular - latin-ext_latin */
@font-face {
font-display: swap; /* Check https://developer.mozilla.org/en-US/docs/Web/CSS/@font-face/font-display for other options. */
font-family: 'Lato';
font-style: normal;
font-weight: 400;
src: url('fonts/lato-v23-latin-ext_latin-regular.woff2') format('woff2'), /* Chrome 36+, Opera 23+, Firefox 39+ */
url('fonts/lato-v23-latin-ext_latin-regular.woff') format('woff'); /* Chrome 5+, Firefox 3.6+, IE 9+, Safari 5.1+ */
(...)
$font-family-sans-serif: 'Lato';
}
```
In my environment, the fonts are still downloaded from the google api in the fonts folder: `/site_libs/bootstrap/fonts`
This screenshot also shows that the api is still in use:
<img width="417" alt="image" src="https://user-images.githubusercontent.com/41738984/219420144-118f9a6a-a6b3-43c0-98f9-7f3504c61701.png">
From a user perspetive, it would be most helpful to have a variable that ensures that no font is used via an api. Any other approach to ensure that only local fonts are used would likewise be appreciated.
As a side-note: This is particularily relevant in Germany, because there is a legal issue using google fonts that are included via the API. Therefore, this issue should be relevant for a larger group of users.
I raised this issue [here](https://stackoverflow.com/questions/75464776/how-to-override-the-default-font-using-locally-stored-fonts-in-themes/75472368#75472368).
My environment:
- WSL2 Ubuntu 20.04
- VS Code 1.75.1
- Quarto Version: 1.2.335
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2023-02-16T16:04:10Z",
"creator": "Klesel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4387,
"state": "closed",
"title": "Quarto Website: Using local fonts (Google Fonts)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4387"
} |
```powershell
mkdir tests
cd tests
echo "# test" >> test.qmd
```
Rendering ok
```powershell
> quarto render test.qmd
pandoc
to: html
output-file: test.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
Output created: test.html
```
Publishing is not ok
````powershell
> quarto publish quarto-pub .\test.qmd
? Publish with account [email protected] (Y/n) » Yes
? Publish with name 'test'? (Y/n) » Yes
[>] Creating quarto-pub document
Rendering for publish:
ERROR: The --site-url flag can only be used when rendering projects.
Error: The --site-url flag can only be used when rendering projects.
at validateDocumentRenderFlags (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-shared.ts:268:15)
at render (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-shared.ts:98:3)
at async renderForPublish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/publish/publish.ts:164:24)
at async renderForPublish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/publish/common/publish.ts:248:22)
at async handlePublish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/publish/common/publish.ts:117:24)
at async publishDocument (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/publish/publish.ts:260:36)
at async publish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/publish/cmd.ts:282:9)
at async doPublish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/publish/cmd.ts:195:7)
at async publishAction (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/publish/cmd.ts:258:7)
at async Command.fn (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/publish/cmd.ts:153:11)
````
By adding a `_quarto.yml` to make it a project, it works ok
```powershell
> echo "project:" > _quarto.yml
> echo " type: default" >> _quarto.yml
> cat .\_quarto.yml
project:
type: default
>
> quarto publish quarto-pub .\test.qmd
? Publish with account [email protected] (Y/n) » Yes
? Publish with name 'test-29f7'? (Y/n) » Yes
[>] Creating quarto-pub document
Rendering for publish:
pandoc
to: html
output-file: test.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
[>] Preparing to publish document
[>] Uploading files (complete)
[>] Deploying published document
[>] Published document: https://cderv.quarto.pub/test-29f7
[>] Account site updated: https://cderv.quarto.pub
```
**Do no forget to go to https://quarto.pub to remove the testing document published** | {
"assignee": null,
"comments": 2,
"created_at": "2023-02-16T12:11:17Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"publishing"
],
"locked": false,
"milestone": "v1.3",
"number": 4384,
"state": "closed",
"title": "publishing to quarto-pub does not work without a Quarto project",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4384"
} |
````markdown
---
title: "test"
format: html
keep-md: true
---
```{python}
import numpy as np
import pandas as pd
```
```{python}
#| label: fig-series
#| fig-cap: Tests Series
ts = pd.Series(np.random.randn(1000), index=pd.date_range('1/1/2000', periods=1000))
ts = ts.cumsum()
ts.plot()
```
````
Mardkown intermediate output
````markdown
---
title: "test"
format: html
keep-md: true
---
::: {.cell execution_count=1}
``` {.python .cell-code}
import numpy as np
import pandas as pd
# pd.options.plotting.backend = 'holoviews'
```
:::
::: {#fig-series .cell execution_count=2}
``` {.python .cell-code}
ts = pd.Series(np.random.randn(1000), index=pd.date_range('1/1/2000', periods=1000))
ts = ts.cumsum()
ts.plot()
```
::: {#fig-series-1 .cell-output .cell-output-display execution_count=2}
```
<AxesSubplot: >
```
Tests Series
:::
::: {.cell-output .cell-output-display}
{#fig-series-2}
:::
:::
````
_Originally posted by @cderv in https://github.com/quarto-dev/quarto-cli/issues/4374#issuecomment-1432957906_
| {
"assignee": "cscheid",
"comments": 3,
"created_at": "2023-02-16T11:43:10Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"third-party",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 4382,
"state": "open",
"title": "Correctly caption figures produced with pandas `plot()` method",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4382"
} |
### Bug description
When rendering a qmd document to pdf using Rstudio's (2022.12.0 Build 353) quarto engine (v. 1.2.269) from the command line and using keep-tex, the .tex file permissions are 600, rather than the directory default. This is problematic in my usage case because I rely on group permissions. Knitting / rendering from the GUI interface makes no difference.
Linux: Ubuntu 22.04.1, texlive 2021.20220204-1, pandoc 3.0.1
**How to replicate**
Start with filename.qmd file with the following content:
```
---
format:
pdf:
keep-tex: true
output:
pdf_document:
keep_tex: true
---
Hello
```
1. Render the file using Rmarkdown: `Rscript -e 'rmarkdown::render("filename.qmd")'`, list the file permissions
2. Do the same using quarto render, list file permissions.
I get:
1.
```
-rw-rw-r-- 1 user user 99 Feb 16 13:11 filename.qmd
-rw-rw-r-- 1 user user 2347 Feb 16 13:21 filename.tex
-rw-rw-r-- 1 user user 23111 Feb 16 13:21 filename.pdf
```
2.
```
-rw-rw-r-- 1 user user 99 Feb 16 13:11 filename.qmd
-rw------- 1 user user 4760 Feb 16 13:25 filename.tex
-rw-rw-r-- 1 user user 2702 Feb 16 13:25 filename.pdf
```
Thanks!
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 7,
"created_at": "2023-02-16T11:40:58Z",
"creator": "ucpresearch",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4380,
"state": "closed",
"title": "Wrong linux permissions when rendering",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4380"
} |
### Bug description
I have the following in `_extensions/resources_example`:
```
.
├── _extension.yml
└── resources
└── test_file.pdf
```
`_extension.yml`:
```yaml
title: Quarto issue 4377
author: Toni
version: 1.0.0
quarto-required: ">=1.2.0"
contributes:
format:
common:
format-resources:
- resources/
pdf:
keep: false
```
When I render a document using this extension, this is what happens:
1. The first time, it works. The `resources` dir is copied to the root of the repository.
2. The second time it works.
3. The third time it does not work anymore due to a permission denied error.
The cause is that after the 2nd run, the `resources` dir becomes read-only and the 3d run can not remove the files anymore.
This is the trace:
```
ERROR: PermissionDenied: Permission denied (os error 13), remove '<...>/resources/test_file.pdf'
PermissionDenied: Permission denied (os error 13), remove '<...>/resources/test_file.pdf'
at Object.removeSync (deno:runtime/js/30_fs.js:151:9)
at copyFileSync (file:///Applications/quarto/bin/quarto.js:44975:14)
at copyDirSync (file:///Applications/quarto/bin/quarto.js:45007:13)
at copyTo (file:///Applications/quarto/bin/quarto.js:44920:9)
at processFormatResources (file:///Applications/quarto/bin/quarto.js:68968:17)
at async resourceDependenciesPostProcessor (file:///Applications/quarto/bin/quarto.js:69442:9)
at async renderPandoc (file:///Applications/quarto/bin/quarto.js:69679:13)
at async Object.onRender (file:///Applications/quarto/bin/quarto.js:79336:32)
at async renderFiles (file:///Applications/quarto/bin/quarto.js:78709:21)
at async render (file:///Applications/quarto/bin/quarto.js:79023:21)
```
This is on mac but it has been reproduced on Linux as well.
| {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2023-02-16T10:21:34Z",
"creator": "tverbeiren",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4377,
"state": "closed",
"title": "Using a directory in `format-resources` for extensions causes 'permission denied'",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4377"
} |
Following #3294 and its fix #3433
this is supposed to work
````yaml
---
title: "test"
format: html
keep-md: true
---
```{mermaid}
%%| fig-cap: Mermaid diagram
%%| fig-align: center
flowchart TB
a --> b
b --> c
```
````
However it is not.
This is because we do in JS now
https://github.com/quarto-dev/quarto-cli/blob/fbc12cbc4f406f02981011544765552e0ea9078a/src/resources/formats/html/mermaid/mermaid-init.js#L215-L224
but somehow we have more div than expected. The `layout-align` is one div above.
This is the intermediate md
````markdown
---
title: "test"
format: html
keep-md: true
---
:::{.cell layout-align="center"}
:::{.cell-output-display}
:::{}
:::{}
<pre class="mermaid mermaid-js">flowchart TB
a --> b
b --> c
</pre>
:::
Mermaid diagram
:::
:::
:::
````
and the HTML rendered in preview
````
<div class="cell" data-layout-align="center">
<div class="cell-output-display">
<div>
<div>
<svg ...>(SVG CONTENT</svg>
</div>
<p>Mermaid diagram</p>
</div>
</div>
</div>
````
@cscheid I let you see this because
* Either we need to add one more parentElement
```diff
-const div = svg.parentElement.parentElement.parentElement;
+const div = svg.parentElement.parentElement.parentElement.parentElement;
```
* We need to see why we create those empty div in the markdown - maybe there is one more that we expect.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4375
<div type='discussions-op-text'>
<sup>Originally posted by **wilcar** February 16, 2023</sup>
How can I center a mermaid diagram in a html document ?</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2023-02-16T08:48:39Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"crossref",
"mermaid"
],
"locked": false,
"milestone": "v1.4",
"number": 4376,
"state": "open",
"title": "Center mermaid diagram in a html document with `fig-align` does not work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4376"
} |
### Bug description
When using Python via `vscode` Jupyter Notebook, adding the `label` and `fig-cap` to respective code cell not rendering properly in website project.
Expected one caption per figure but website project renders like subcaption, see image below.
Reproducible notebook here:
https://github.com/lgonzalezsa/hello_quarto/blob/test_website/test/website/testing.ipynb
My environment is:
Linux: Pop_OS! 22.04 6.0.12-76060006-generic
vscode:
Version: 1.75.1
Commit: 441438abd1ac652551dbe4d408dfcec8a499b8bf
Date: 2023-02-08T21:35:30.018Z
Electron: 19.1.9
Chromium: 102.0.5005.194
Node.js: 16.14.2
V8: 10.2.154.23-electron.0
OS: Linux x64 6.0.12-76060006-generic
Sandboxed: No
quarto v1.2.335
[✓] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Up to date v2023.02 v2023.02
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 8,
"created_at": "2023-02-16T04:15:00Z",
"creator": "lgonzalezsa",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": "v1.4",
"number": 4374,
"state": "open",
"title": "Python figure cross-reference missing caption and creating subcaption",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4374"
} |
### Bug description
I'm using a lua filter I got from [here](https://stackoverflow.com/a/73787848/13945974) to change the orientation of certain pages so that the figures within them end up larger, but they end up the same size as in the portrait pages. Increasing `out-width` doesn't help.
[2023-02-16_quarto.qmd.zip](https://github.com/quarto-dev/quarto-cli/files/10750788/2023-02-16_quarto.qmd.zip)
[2023-02-16_quarto.docx](https://github.com/quarto-dev/quarto-cli/files/10750790/2023-02-16_quarto.docx)
[docx-landscape.lua.zip](https://github.com/quarto-dev/quarto-cli/files/10750791/docx-landscape.lua.zip)
Quarto version: 1.2.313
Mac 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": 1,
"created_at": "2023-02-16T00:43:04Z",
"creator": "shirdekel",
"is_pull_request": false,
"labels": [
"bug",
"triaged-to"
],
"locked": false,
"milestone": "v1.4",
"number": 4373,
"state": "open",
"title": "Figures not adapting width for landscape",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4373"
} |
### Bug description
Currently, with Quarto 1.3.203, publish options still list RStudio Connect:
```
quarto publish
❯ Quarto Pub
GitHub Pages
RStudio Connect
Netlify
```
That should be updated to Posit Connect. I _think_ these are the relevant spots: https://github.com/search?q=repo%3Aquarto-dev%2Fquarto-cli+%22RStudio+Connect%22&type=code.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-02-15T20:23:32Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4371,
"state": "closed",
"title": "`quarto publish` RStudio -> Posit Connect",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4371"
} |
### Bug description
The following file seems to return an error (LaTeX Error: Not in outer par mode) only with `echo:false`. Tested on MacOS and Windows.
````
---
format: pdf
---
::: {#fig-12 layout-ncol=2}
```{r}
#| fig-cap: "f1"
#| echo: false
plot(1)
```
```{r}
#| fig-cap: "f2"
plot(2)
```
Figure
:::
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2023-02-15T18:43:17Z",
"creator": "AQLT",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4370,
"state": "open",
"title": "PDF side-by-side figure with caption error with echo: false",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4370"
} |
### Bug description
I'm getting to the point in my book where I need to show algorithms. I couldn't get [Christophe Dervieux's Rmd instructions](https://rpubs.com/cderv/pseudocodejs) to work, so I made a reprex repo (reporex?).
https://github.com/topepo/quarto-pseudocode-test
https://topepo.github.io/quarto-pseudocode-test/
There was some weirdness. When I first compiled it, the `js` block wanted me to install jupyter (no thanks). I moved the same example code to the (private) book repo and rendered it so that I could take a screen shot.
After that, my reporex rendered without the jupyter request but the algorithm doesn't show up.
Also, when it does show up, the equations are not rendered (see the screen shot in the reporex).
### 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": 12,
"created_at": "2023-02-15T18:42:23Z",
"creator": "topepo",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 4369,
"state": "open",
"title": "pseudocode.js algorithms",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4369"
} |
From #4350, it seems that we can't set v8-flags with released versions of quarto (as opposed to versions running off of the git repo). This is a problem since setting v8-flags is how we increase the heap size.
Should we proactively set a larger max heap size based on a guess of the system's max memory? | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-02-15T18:30:24Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 4368,
"state": "closed",
"title": "OOM workarounds: quarto releases don't appear to v8-flags settings",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4368"
} |
See #4356. We should detect these in a filter and either emit a warning or automatically enable `number-sections: true`. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2023-02-15T15:38:18Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 4364,
"state": "open",
"title": "Section crossref in pdf format need `number-sections: true`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4364"
} |
### Bug description
Running
```{r}
ojs_define(my_ojs = my_sw)
```
yields error message:
> Error in ojs_define(my_ojs = my_sw) :
could not find function "ojs_define"
I've tried this on
- Windows 10 Enterprise ; RStudio 2022.12.0 ; Quarto v 1.1.179
- Windows 10 Enterprise ; RStudio 2022.12.0+353 ; Quarto 1.3.202
- Ubuntu 22.04.1 LTS ; RStudio 2022.12.0 Build 353 ; Quarto 1.2.269
Qmd document attached. Had to save as .md to get past the GitHub filters. [foo_quarto.md](https://github.com/quarto-dev/quarto-cli/files/10744471/foo_quarto.md)
Any help greatly appreciated.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2023-02-15T15:24:49Z",
"creator": "libjohn",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4363,
"state": "closed",
"title": "cannot find ojs_define function within RStudio quarto doc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4363"
} |
### Bug description
````md
---
title: "Untitled"
format: pdf
editor: visual
---
Please see @ref1.
## Quarto {#ref1}
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
````
I hope I'm not making a simple mistake, but the code autocompletion does not recognize `ref1` in visual mode, nor is the document properly generating the link..
RStudio
2022.12.0 Build 353
```{r}
> Sys.info()
sysname
"Darwin"
release
"22.3.0"
version
"Darwin Kernel Version 22.3.0: Thu Jan 5 20:53:49 PST 2023; root:xnu-8792.81.2~2/RELEASE_X86_64"
nodename
"Matthews-MacBook-Pro-2.local"
machine
"x86_64"
login
"root"
user
"matthewson"
effective_user
"matthewson"
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-02-15T00:35:19Z",
"creator": "matthewgson",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4356,
"state": "closed",
"title": "Cross reference does not work on headings (pdf)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4356"
} |
For a `revealjs` document format, Mathjax is configured as follows
```
math: {
mathjax: 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js',
...........
},
},
```
while for a `book`, we get a more recent version of MathJax
```
<script src="[https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml-full.js](view-source:https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml-full.js)" type="text/javascript"></script>
```
Is it intentional, or should it be considered a bug?
Can I specify the version of MathJax I want to use? | {
"assignee": "cderv",
"comments": 4,
"created_at": "2023-02-14T16:46:01Z",
"creator": "sbrisard",
"is_pull_request": false,
"labels": [
"upstream",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 4493,
"state": "open",
"title": "Project format `revealjs` uses old version of MathJax",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4493"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4349
<div type='discussions-op-text'>
<sup>Originally posted by **kris-brown** February 14, 2023</sup>
I'm not sure what the cause of this new behavior is, but after adding a couple hundred pages to my website (mostly text and quite short) I began getting the below error upon `quarto render` with both the current release and pre-release versions. StackOverflow says this message is usually associated with a memory leak. After the error I can `quarto preview` and see the built website, but things like full text search are broken. Is there anything I can check on my end to debug this?
```
...
748/749] docs/blog/index.qmd
[749/749] index.qmd
<--- Last few GCs --->
[30742:0x128048000] 501878 ms: Mark-Compact 1367.4 (1437.0) -> 1355.3 (1440.7) MB, 1384.1 / 0.0 ms (average mu = 0.136, current mu = 0.016) allocation failure; scavenge might not succeed
[30742:0x128048000] 503297 ms: Mark-Compact 1372.4 (1442.0) -> 1360.7 (1446.2) MB, 1389.6 / 0.0 ms (average mu = 0.081, current mu = 0.021) allocation failure; scavenge might not succeed
<--- JS stacktrace --->
#
# Fatal javascript OOM in Ineffective mark-compacts near heap limit
#
/Applications/quarto/bin/quarto: line 158: 30742 Trace/BPT trap: 5 "${QUARTO_DENO}" ${QUARTO_ACTION} ${QUARTO_DENO_OPTIONS} ${QUARTO_DENO_EXTRA_OPTIONS} "${QUARTO_IMPORT_ARGMAP}" "${QUARTO_TARGET}" "$@"
```</div> | {
"assignee": "cscheid",
"comments": 16,
"created_at": "2023-02-14T16:39:27Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4350,
"state": "closed",
"title": "Fatal javascript OOM in Ineffective mark-compacts near heap limit",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4350"
} |
> Adding figure creation in the test qmd file, we can see that the the figure dir is in another folder containing format in the name
And so now I have it all covered. Probably another issue but related.
The directory with format in the name is created by **rmarkdown** when R chunks are added. I don't think Quarto expect this so not sure we are cleaning this correctly.
When no `output_file` is passed to `rmarkdown::render()`, one is automatically determined considering the `pandoc.to` format.
````r
# determine the output file for a pandoc conversion
pandoc_output_file <- function(input, pandoc_options) {
to <- strsplit(pandoc_options$to, "[+-]")[[1]][[1]]
ext <- pandoc_output_ext(pandoc_options$ext, to, input)
output <- paste0(xfun::sans_ext(input), ext)
basename(output)
}
````
With `to` being `customwriter.lua`, the output file will have a `.customwriter` suffix as we can see in above comments
Then the files where to store figures for **knitr** is computed based on `output_file`
````r
files_dir_slash <- file.path(output_dir, knitr_files_dir(basename(output_file)))
````
which will lead to the other folder `customwriter-yaml.customformat_files` when R code are into this.
I believe this will happen with any format no known by rmarkdown function `pandoc_output_ext`
````r
pandoc_output_ext <- function(ext, to, input) {
if (!is.null(ext)) return(ext)
if (to %in% c("latex", "beamer")) return(".pdf")
if (to %in% c("html", "html4", "html5", "s5", "slidy", "slideous", "dzslides", "revealjs"))
return(".html")
if (to == "markdown" && tolower(xfun::file_ext(input)) != "md") return(".md")
paste0(".", to)
}
````
I'll probably look into that in another issue too, but that explains the behavior and differences seen above
_Originally posted by @cderv in https://github.com/quarto-dev/quarto-cli/issues/4260#issuecomment-1421667821_
| {
"assignee": "cderv",
"comments": 1,
"created_at": "2023-02-14T15:48:14Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4347,
"state": "open",
"title": "Specific handling for custom writer lua file for R Markdown processing",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4347"
} |
I am trying to render a pdf using the asc extention: https://github.com/quarto-journals/acs
I am running quarto version 1.2.335 on windowsWindows 10 Enterprise Version 10.0.19044 Build 19044 through Rstudio.
I set up a new dir containing the extention template:
`quarto use template quarto-journals/acs`
Then render:
`quarto render template.qmd --to acs-pdf`
I get error:
`ERROR: The filename, directory name, or volume label syntax is incorrect. (os error 123), stat 'D:\Repositories\bugErrorHelp\template\_extensions\quarto-journals\acs\_extensions\quarto-ext\latex-environment\D:\Repositories\bugErrorHelp\template\_extensions\quarto-journals\acs\_extensions\quarto-ext\latex-environment\latex-environment.lua'`
It looks like quarto concatinating the full path of latex-environment.lua file into the directory path of the file resulting in an unfindable path. I can't see anywhere where the path might manually be tweeked.
The extention offeres an html render as well, which works just fine.
As this bug seems not to be previosly reported I wonder if it is an issue with my machine.
| {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2023-02-14T10:46:16Z",
"creator": "M-Russell",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4346,
"state": "closed",
"title": "Extention filename incorrect OS error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4346"
} |
Quarto gives the option to make Python/R variables available to OJS via the `ojs_define()` function. However, when working inside a Jupyter notebook `ojs_define()` is obviously not defined. Current workaround requires converting to .qmd first then adding a Python/R snippet using `ojs_define()` and then rendering the .qmd file. | {
"assignee": null,
"comments": 2,
"created_at": "2023-02-13T22:13:35Z",
"creator": "IliasAarab",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4344,
"state": "closed",
"title": "Using ojs_define() inside a Jupyter notebook",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4344"
} |
Qualified paths were added in https://github.com/quarto-dev/quarto-cli/pull/2429
* https://github.com/quarto-dev/quarto-cli/blob/main/src/core/qualified-path.ts
Currently, tests are not made for windows: https://github.com/quarto-dev/quarto-cli/blob/main/tests/unit/paths/qualified-path.test.ts
In #4099, I'll ignore tests for now until this is fixed. | {
"assignee": "cderv",
"comments": 0,
"created_at": "2023-02-13T19:45:06Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"windows"
],
"locked": false,
"milestone": "Future",
"number": 4339,
"state": "open",
"title": "Adapt tests for qualified paths for Windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4339"
} |
From our `tests` folder
````
quarto render docs\smoke-all\2023\01\05\notebook-preview-complex.qmd --to html
````
This throws an error
````
ERROR: La syntaxe du nom de fichier, de répertoire ou de volume est incorrecte. (os error 123), stat 'docs\smoke-all\2023\01\05\https:\www.kaggle.com\code\kanncaa1\data-sciencetutorial-for-beginners'
Error: La syntaxe du nom de fichier, de répertoire ou de volume est incorrecte. (os error 123), stat 'docs\smoke-all\2023\01\05\https:\www.kaggle.com\code\kanncaa1\data-sciencetutorial-for-beginners'
at Object.lstatSync (deno:runtime/js/30_fs.js:305:9)
at existsSync (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/vendor/deno.land/[email protected]/fs/exists.ts:75:10)
at Array.filter (<anonymous>)
at Object.complete (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render.ts:327:24)
at async Object.onPostProcess (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:568:28)
at async renderFiles (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:524:7)
at async render (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-shared.ts:101:18)
at async Command.fn (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/cmd.ts:193:26)
at async Command.execute (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7)
at async quarto (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/quarto.ts:111:3)
````
We are taking the url from `notebook-view` config
https://github.com/quarto-dev/quarto-cli/blob/main/tests/docs/smoke-all/2023/01/05/notebook-preview-complex.qmd#L23-L26
and somehow create a path with it
````
docs\smoke-all\2023\01\05\https:\www.kaggle.com\code\kanncaa1\data-sciencetutorial-for-beginners
````
which is a non valid PATH and fails on Windows when resources file are computed
https://github.com/quarto-dev/quarto-cli/blob/9e09dedabadc4a37bf4ff5aeb61862e3ca4a257d/src/command/render/render.ts#L326-L329
| {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2023-02-13T16:17:07Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 4337,
"state": "closed",
"title": "`notebook-view` appends URL to figure path somewhere and this error on Windows ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4337"
} |
### Bug description
I've been working on a custom code syntax theme and have run into a couple of limitations. I made [a repo with a basic blog website](https://github.com/gadenbuie/quarto-reprex/tree/website-syntax-styles) that demonstrates the problem. The links below are to specific commits or diffs (I also described the problems/steps [in the commit history](https://github.com/gadenbuie/quarto-reprex/commits/website-syntax-styles)).
1. pandoc's default color scheme is [inlined in the rendered website content](https://github.com/gadenbuie/quarto-reprex/blob/587c29f5cf001e4fc2043c2d72a4b77ed8906957/syntax-styles/_site/posts/post-with-code/index.html#L59-L87).
* The default styles contain `font-weight` and `font-style` properties.
* If a custom theme [sets `italic: false` for these tokens](https://github.com/gadenbuie/quarto-reprex/commit/8407c0366dda2dd97e5c2c12da6cfe9839d8db8b#diff-1b543bdd0b13564bb5975b178bee67565f30217b9cca4bd48d27b722d2e38a24), the `font-style: italic` property [is removed in quarto-syntax-highlighting.css](https://github.com/gadenbuie/quarto-reprex/commit/8407c0366dda2dd97e5c2c12da6cfe9839d8db8b#diff-4420bcdaeeb0c6e5a17f8da212ecce3c6a7f5f3d62d3f838377967ec53aaa392), but this does not disable the italics [due to the inlined rules](https://github.com/gadenbuie/quarto-reprex/commit/39a96a16ca947a14d744a8fb04f5905cb8319e37).
* I came up with [a (hopefully temporary) solution](https://github.com/gadenbuie/quarto-reprex/commit/7014a645229a87cd1056943abac9fc53dbe84fd4) to remove the `code span.xx` rules in the browser with JavaScript. Alternatively, one can write additional custom rules that override the inlined rules.
2. The syntax `.theme` to `quarto-syntax-highlighting.css` translation [doesn't include token background colors](https://github.com/gadenbuie/quarto-reprex/commit/80eef62d32c19513cafe4540255351abbe7f1d14). These aren't very common, but I'm a fan of subtle background colors on specific tokens and use them in my site.
```
# System Version: macOS 13.0 (22A380)
quarto --version
1.2.335
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-02-13T14:10:59Z",
"creator": "gadenbuie",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4334,
"state": "closed",
"title": "Blog posts include inlined CSS styles that are hard to overwrite",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4334"
} |
From https://github.com/quarto-dev/quarto-cli/discussions/2263#discussioncomment-4942301
See if we can integrate part of the doc of [reveal/multiplex](https://github.com/reveal/multiplex) about setting things up. | {
"assignee": "cderv",
"comments": 0,
"created_at": "2023-02-13T10:13:12Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4495,
"state": "open",
"title": "Improve doc about multiplex revealjs extension",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4495"
} |
### Bug description
The search bar for Quarto websites ignores code before the first section heading.
**Reprex:** Create a template Quarto site and adjust the `.qmd` per below so that there is `library(dplyr)`, followed by a section heading, then `library(tidyr)`. After rendering, a site search for `lib` finds `library(tidyr)` but not `library(dplyr)`.
````
---
title: "rprex"
---
This is a Quarto website.
To learn more about Quarto websites visit <https://quarto.org/docs/websites>.
```{r}
library(dplyr)
```
## Heading
```{r}
library(tidyr)
```
````
<img width="234" alt="Screenshot 2023-02-12 at 20 49 40" src="https://user-images.githubusercontent.com/32419319/218336272-f33beef2-f62e-4a60-b265-df7c6742c924.png">
RStudio Version 2022.12.0+353
Quarto v1.3.189
MacOS 13.2 (22D49)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 0,
"created_at": "2023-02-12T21:00:57Z",
"creator": "cgoo4",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4329,
"state": "closed",
"title": "Site search results exclude code before a section heading",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4329"
} |
### Bug description
When trying to insert paged table: the output is too big to fit on the screen:
[Source to reproduce](https://pastebin.com/A2zTMfqY)
Result with 100% page zoom:
Result with 50% page zoom:
Session info:
```
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Arch Linux
Matrix products: default
BLAS: /usr/lib/libopenblas.so.0.3
LAPACK: /usr/lib/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] quarto_1.2 httpgd_1.3.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 ps_1.7.2 digest_0.6.31 later_1.3.0 parallelly_1.33.0
[6] jsonlite_1.8.4 evaluate_0.19 rlang_1.0.6 cli_3.5.0 rstudioapi_0.14
[11] rmarkdown_2.19 tools_4.2.2 yaml_2.3.6 fastmap_1.1.0 xfun_0.36
[16] parallel_4.2.2 compiler_4.2.2 processx_3.8.0 systemfonts_1.0.4 htmltools_0.5.4
[21] knitr_1.41
```
Rstudio version:
```
RStudio 2023.03.0-daily+265 "Cherry Blossom" Daily (df867f7d2dc6f7a6ddad4b6cdea992fa41c182a1, 2023-01-20) for Ubuntu Jammy
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) rstudio/2023.03.0-daily+265 Chrome/108.0.5359.179 Electron/22.0.3 Safari/537.36
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-02-12T18:48:22Z",
"creator": "davidbudzynski",
"is_pull_request": false,
"labels": [
"bug",
"duplicate",
"verify-fixed"
],
"locked": false,
"milestone": null,
"number": 4328,
"state": "closed",
"title": "Paged tables too big to fit on revealjs slides",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4328"
} |
To reproduce my error, run `quarto render` | {
"assignee": null,
"comments": 5,
"created_at": "2023-02-12T16:58:36Z",
"creator": "Waterkin",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4326,
"state": "closed",
"title": "LaTeX Error: Cannot determine size of graphic in loss.webp (no BoundingBox).",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4326"
} |
### Bug description
_No response_
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2023-02-12T03:24:25Z",
"creator": "mikheyev",
"is_pull_request": false,
"labels": [
"bug",
"articles"
],
"locked": false,
"milestone": "v1.3",
"number": 4324,
"state": "closed",
"title": "Table endnotes don't work in margins",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4324"
} |
I would like to figure out a way to make presenter notes for my Quarto presentations kept private and something I could add to my .gitignore. Perhaps the notes could be created in a child document that can be rendered with the main presentation, but I don't have to bare my soul (and all the reminders to myself) in the code of my actual slides.
| {
"assignee": null,
"comments": 6,
"created_at": "2023-02-10T19:38:52Z",
"creator": "kmasiello",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 4318,
"state": "open",
"title": "FR: Allow for presenter notes in Quarto presentations to be kept private",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4318"
} |
````
---
format: html
---
```{r}
#| include: false
library(tidyverse)
library(gt)
```
```{r}
#| echo: false
#| tbl-cap: "Caption"
#| label: tbl-test
dat <- tribble(~a, ~x, ~y, ~z,
"A", 1, 12, 13,
"B", 2, 9, 11)
dat %>%
gt() %>%
tab_spanner(
label = "Subheader",
columns = c(x, y)
)
```
@tbl-test
````
Produced output:
<img width="1153" alt="image" src="https://user-images.githubusercontent.com/285675/218155441-d762063a-3043-43f6-8543-8dd200e73854.png">
Desired output:
<img width="545" alt="image" src="https://user-images.githubusercontent.com/285675/218155490-0e0014c7-5dde-4ba8-8b6a-9a39f4405732.png">
This is either CSS or our table processing failing in the presence of spanners. Maybe a combination of both, since it only happens when we inject a caption. | {
"assignee": "cscheid",
"comments": 10,
"created_at": "2023-02-10T17:21:00Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"tables"
],
"locked": false,
"milestone": "v1.3",
"number": 4316,
"state": "closed",
"title": "gt table spanners and quarto captions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4316"
} |
### Bug description
Hello,
I try to center all figures in my document with a YAML argument so I tried the generic option `fig-align`
````
---
title: "Untitled"
format: html
fig-align: center
---
```{r}
knitr::opts_chunk$get("fig.align")
```
````
But it is not used. However, with the "old" syntax
```
---
title: "Untitled"
format: html
knitr:
opts_chunk:
fig.align: center
---
```
the figures are aligned correctly. Is this the desired behavior? Thanks
RStudio Version 2022.12.0+353 (2022.12.0+353)
Mac OS 13.1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2023-02-10T15:30:55Z",
"creator": "abichat",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 4315,
"state": "open",
"title": "fig-align in YAML doesn't work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4315"
} |
`ojs_define()` is a function that can be used in Quarto cells for R Julia and Python. When used in such chunk, one can't execute the cell interactively because the function only works when rendering the whole document.
However, maybe it would be easier for our integrated tool (IDE, VSCODE, ...) to "ignore" the ojs_define() when running the cell interactively. OJS can't work interactively, but other chunks could.
Do you think this is something feasible and valuable ? Not sure how interactive run of cells works in RStudio IDE or VSCODE, and asking here before opening issue in different repo to track idea.
(I got bitten by that once, and some users too that is why I thought about that) | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-02-10T15:30:01Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 4314,
"state": "open",
"title": "Don't fail running chunk interactively in IDE or VSCODE when `ojs_define()` is present in chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4314"
} |
### Bug description
I am trying to preview a simple docusaurus website on windows 10 thought VSCode but I got the following error:
``` console
$quarto preview
Preparing to preview
Watching files for changes
ERROR: NotFound: program not found
```
I have to say I have no clue which program is not found.
I tried the following:
- Install chromium with `quarto tools install chromium`
- If I preview directly the website with `npm start`, it is working. So docusaurus installation seems fine.
- If I am tring to render/preview the files directly with the integrated button to VS code.
I got the same error:
```console
Preview service running (3985)
ERROR: NotFound: program not found
```
So the error seems linked to quarto.
- I tried to open the exact same setup in WSL and it is working. It is missing something on windows configuration then. But I cannot find what.
- If I am tring to remove `type: docusaurus` in _quarto.yml. It is working. So seems to be linked to quarto and docusaurus integration.
```yml
project:
type: docusaurus
```
Can you help me with this error ? Thanks a lot.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 11,
"created_at": "2023-02-10T10:51:58Z",
"creator": "FabienSe",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": null,
"number": 4312,
"state": "closed",
"title": "Impossible to start preview of docusaurus website",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4312"
} |
In Quarto website
Internal links to level 3 titles leads to the paragraph that follows the title and not to the title itself. | {
"assignee": null,
"comments": 1,
"created_at": "2023-02-10T10:42:29Z",
"creator": "wilcar",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4311,
"state": "closed",
"title": "internal link offset",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4311"
} |
### Bug description
Hi,
I have this input qmd file
~~~~
---
title: "Test Kakumbi 2018-2020"
format:
html:
toc-depth: 5
toc-location: left
footnotes-hover: true
---
<img src="file:///home/aborruso/lavagna/tmp file.png" style="width: 100%;"/>
~~~~
And this setting file
~~~~
sidebar: false
navbar: false
embed-resources: true
~~~~
When I run
```
quarto render input.qmd --metadata-file settings.yml
```
I have this error
```
pandoc: /home/aborruso/lavagna/tmp%20file.png: withBinaryFile: does not exist (No such file or directory)
```
It seems related to [this pandoc issue](https://github.com/jgm/pandoc/issues/7819#issuecomment-1008220337), but I think there is something to do here in quarto to manage it.
I'm using Debian 11 and quarto 1.3.189
Thank you
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-02-10T10:03:32Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4310,
"state": "closed",
"title": "spaces in filenames don't seem to always be handled correctly: a special embed-resources case",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4310"
} |
* Remove IJulia from your environment `import Pkg; Pkg.rm("IJulia")`
* Run a document with Julia in command line
````markdown
---
title: Julia
format: html
jupyter: julia-1.8
---
```{julia}
b = 2
```
````
```
> quarto render test.qmd
Starting julia-1.8 kernel...ERROR:
Kernel died before replying to kernel_info
NativeCommandExitException: Program "quarto.exe" ended with non-zero exit code: 1.
````
IJulia is missing so I expect it to fail but no hint about that. Also this is same short error message as in https://github.com/quarto-dev/quarto-cli/issues/2539#issuecomment-1380522200
Doing the `--no-execute-daemon` will make the error more clear
````
> quarto render test.qmd --no-execute-daemon
Starting julia-1.8 kernel...ERROR: LoadError: ArgumentError: Package IJulia not found in current path.
- Run `import Pkg; Pkg.add("IJulia")` to install the IJulia package.
Stacktrace:
[1] macro expansion
@ .\loading.jl:1163 [inlined]
[2] macro expansion
@ .\lock.jl:223 [inlined]
[3] require(into::Module, mod::Symbol)
@ Base .\loading.jl:1144
in expression starting at C:\Users\chris\.julia\packages\IJulia\6TIq1\src\kernel.jl:1
2023-02-10 10:55:48,405 - traitlets - ERROR - Error occurred while starting new kernel client for kernel e17486eb-37df-40ba-b972-59a1ab07821c: Kernel died before replying to kernel_info
Kernel died before replying to kernel_info
NativeCommandExitException: Program "quarto.exe" ended with non-zero exit code: 1.
````
So after that we install Julia with `import Pkg; Pkg.add("IJulia")`
and then we try to render again using the usual
```
> quarto render test.qmd
Starting julia-1.8 kernel...Done
Executing 'test.ipynb'
Cell 1/1...Done
pandoc
to: html
output-file: test2.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: Julia
jupyter: julia-1.8
Output created: test.html
```
This time it works.
So it seems to me that we are not passing all the error message when the daemon is used, as we get the cause only when `--no-execute-daemon` is passed, but the fix (installing the IJulia package) is fixing the issue with using the daemon also.
Sharing in case we can improve this | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2023-02-10T10:02:51Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 4309,
"state": "open",
"title": "Show missing IJulia package error when daemon is used to and not only when `no-execute-daemon` is used",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4309"
} |
For what it's worth I've found RStudio to be _currently_ inconsistent with chunk label prefixes as shown in the following ASCII encoded MWEs. I don't have chromium or tinytex installed on `quarto tools check`. Hopefully this is going to be fixed soon.
````markdown
---
title: "MWE 1"
format: html
---
### Environment
- R Version 4.2.1
- RStudio desktop 2022.12.0.353"
- Linux 22.10 (Kinetic Kudu)
### Output
Cross referencing works for @fig-ans and @fig-dag and both labels are picked up by the visual editor crossref widget.
```{r}
#| label: fig-ans
#| fig-cap: First caption
#| echo: false
with(anscombe, plot(x2,y2))
```
------------------------------------------------------------------------
```{dot}
//| label: fig-dag
//| fig-cap: Second caption
digraph ER{
cause -> effect
}
```
`````
````markdown
---
title: "MWE 2"
format: html
---
### Environment
- R Version 4.2.1
- RStudio desktop 2022.12.0.353"
- Linux 22.10 (Kinetic Kudu)
### Output
This compiles with the cross reference working for @fig-ans. The second chunk label is picked up by the visual editor crossref widget but the crossref fails with @fig-dag and no caption is generated.
```{r}
#| label: fig-ans
#| fig-cap: First caption
#| echo: false
with(anscombe, plot(x2,y2))
```
------------------------------------------------------------------------
```{dot}
#| label: fig-dag
#| fig-cap: Second caption
digraph ER{cause -> effect}
```
`````
````markdown
---
title: "MWE 3"
format: html
---
### Environment
- R Version 4.2.1
- RStudio desktop 2022.12.0.353"
- Linux 22.10 (Kinetic Kudu)
### Output
This fails to compile with
- unexpected token '/'
- unexpected token '/'
- unexpected token '\|'
```{r}
//| label: fig-ans
//| fig-cap: First caption
//| echo: false
with(anscombe, plot(x2,y2))
```
------------------------------------------------------------------------
```{dot}
//| label: fig-dag
//| fig-cap: Second caption
digraph ER{
cause -> effect
}
```
````
_Originally posted by @ar0berts in https://github.com/quarto-dev/quarto-cli/issues/1296#issuecomment-1425329710_
| {
"assignee": null,
"comments": 1,
"created_at": "2023-02-10T09:39:26Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4308,
"state": "closed",
"title": "dot diagram inconsistency with chunk label prefixes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4308"
} |
### Bug description
Searching `_*` in Quarto book crashes the browser tab. To reproduce the issue:
1. Go to https://r-pkgs.org/.
1. Type `_*` in the search box.
1. Click any result in the dropdown.
1. In Chrome, the browser tab crashes, showing
```
Aw, Snap!
Something went wrong while displaying this webpage.
Error code: 5
```
In Edge, it shows: This page is having a problem. Error code: **Out of Memory**.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-02-10T07:20:02Z",
"creator": "nanxstats",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4307,
"state": "closed",
"title": "Searching `_*` in Quarto book crashes browser",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4307"
} |
### Bug description
This issue came up earlier today when a student was having problems identifying why their quarto document wasn't able to be rendered.
In particular, the student accidentally spaced the code chunk option one extra, that is:
````
```{sql}
#| label: test multiqueries -5
#| connection: db
-- ^ note the extra space
select 1
```
````
Thus, when the Quarto document was rendered, we were seeing:
```
processing file: my-homework.qmd
Error in yaml::yaml.load(meta, handlers = list(expr = parse_only)) :
Scanner error: mapping values are not allowed in this context at line 2, column 12
Calls: .main ... FUN -> parse_block -> partition_chunk -> <Anonymous>
Execution halted
```
This is a misleading error as it implies that the error falls inside of the document customization header. Instead, the error was related to a code chunk option.
Would it be possible to provide more localized support for bad code chunk specification?
`my-homework.qmd` :
````
---
title: "Example"
format: pdf
engine: knitr
editor: visual
---
```{r}
# install.packages(c("DBI", "RSQLite"))
db = DBI::dbConnect(RSQLite::SQLite(), ":memory:")
```
```{sql}
#| label: test multiqueries -5
#| connection: db
select 1
```
````
---
Version information:
- RStudio: 2022.12.0.353
- Quarto: 1.2.313
- Operating System: macOS
### 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": 9,
"created_at": "2023-02-10T06:08:38Z",
"creator": "coatless",
"is_pull_request": false,
"labels": [
"documentation",
"enhancement",
"upstream"
],
"locked": false,
"milestone": "v1.4",
"number": 4306,
"state": "open",
"title": "Unclear error message when using code chunk options with yaml and an extra space is present",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4306"
} |
I hope this is not an issue specific to my machine/setup, but I have observed the following behavior. When quarto (via `quarto run`) is used to install the rmarkdown package on a windows machine, it seems to freeze up indefinitely. Other packages (e.g., magrittr) install fine via `quarto run`.
Call: `quarto run code.R`
File `code.R`:
```
install.packages(pkgs = 'rmarkdown', character.only = TRUE, repos = 'http://cran.us.r-project.org', type = "win.binary")
```
The problem seems to occur at step 26 within `utils::install.packages`, specifically the call to ` .install.winbinary()`:
```
if (.Platform$OS.type == "windows") {
if (startsWith(type, "mac.binary"))
stop("cannot install macOS binary packages on Windows")
if (type %in% "win.binary") {
.install.winbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
dependencies = dependencies, libs_only = libs_only,
quiet = quiet, ...)
return(invisible())
}
have_spaces <- grep(" ", pkgs)
if (length(have_spaces)) {
p <- pkgs[have_spaces]
dirs <- shortPathName(dirname(p))
pkgs[have_spaces] <- file.path(dirs, basename(p))
}
pkgs <- gsub("\\", "/", pkgs, fixed = TRUE)
}
else {
if (startsWith(type, "mac.binary")) {
if (!grepl("darwin", R.version$platform))
stop("cannot install macOS binary packages on this platform")
.install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,
method = method, available = available, destdir = destdir,
dependencies = dependencies, quiet = quiet, ...)
return(invisible())
}
if (type %in% "win.binary")
stop("cannot install Windows binary packages on this platform")
if (!file.exists(file.path(R.home("bin"), "INSTALL")))
stop("This version of R is not set up to install source packages\nIf it was installed from an RPM, you may need the R-devel RPM")
}
```
Quarto version 1.1.189.
Output of `R.version`:
```
platform x86_64-w64-mingw32
arch x86_64
os mingw32
crt ucrt
system x86_64, mingw32
status
major 4
minor 2.1
year 2022
month 06
day 23
svn rev 82513
language R
version.string R version 4.2.1 (2022-06-23 ucrt)
nickname Funny-Looking Kid
``` | {
"assignee": null,
"comments": 3,
"created_at": "2023-02-09T17:09:09Z",
"creator": "pecanka",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4300,
"state": "closed",
"title": "Quarto run freezes when used to install rmarkdown (via quarto run)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4300"
} |
### Bug description
When working with centered slides in RevealJS, aside and footnote sections overlap with content.
See the example and screenshot below.
Workaround: add a couple `<br>` blocks. :/
Operating system: macOS
````md
---
format:
revealjs:
transition: slide
controls: true
controls-layout: bottom-right
center: true
navigation-mode: vertical
---
## OCI Runtime
- Bundle
- Root FS
- Config (command, limits, mounts, etc)
- Runtime starts the container ^[_(usually) an isolated Linux process, VM, etc_]
````
<img width="1345" alt="Screenshot 2023-02-09 at 17 21 37" src="https://user-images.githubusercontent.com/1226384/217872591-744853e6-af95-4145-8d60-f41cbc74c602.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": "dragonstyle",
"comments": 0,
"created_at": "2023-02-09T16:23:37Z",
"creator": "sagikazarmark",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4297,
"state": "closed",
"title": "Centered reveal slide content overlap with aside and footnotes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4297"
} |
### Bug description
I'm not exactly sure what is the culprit.
Steps to reproduce:
- Clone `fastai/nbdev`
- Install nbdev if you don't have it already.
- `pip install -e .[dev]` in the `nbdev` directory.
- run `nbdev_docs`. It will fail towards the end:
```
[ 1/42] index.qmd
[ 2/42] explanations/index.qmd
WARNING: File /ssd/xl0/work/code/nbdev/_proc/explanations/config.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/explanations/why_nbdev.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/explanations/directives.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/explanations/docs.ipynb in the listing 'listing' contains no metadata.
[ 3/42] explanations/config.ipynb
[ 4/42] explanations/why_nbdev.ipynb
[ 5/42] explanations/directives.ipynb
[ 6/42] explanations/docs.ipynb
[ 7/42] blog/index.qmd
[ 8/42] blog/posts/2022-07-28-nbdev2/index.qmd
[ 9/42] blog/posts/2022-11-07-spaces/index.qmd
Starting python3 kernel...Done
Executing 'index.ipynb'
Cell 1/1...Done
[10/42] blog/posts/2022-08-25-jupyter-git/index.qmd
[11/42] getting_started.ipynb
[12/42] migrating.ipynb
[13/42] api/01_config.ipynb
[14/42] api/17_serve.ipynb
[15/42] api/index.qmd
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/01_config.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/17_serve.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/12_test.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/07_merge.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/18_release.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/02_maker.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/08_showdoc.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/09_frontmatter.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/03_process.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/05_doclinks.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/14_quarto.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/11_clean.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/16_migrate.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/15_qmd.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/06_sync.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/04_export.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/10_processors.ipynb in the listing 'listing' contains no metadata.
WARNING: File /ssd/xl0/work/code/nbdev/_proc/api/13_cli.ipynb in the listing 'listing' contains no metadata.
[16/42] api/12_test.ipynb
[17/42] api/07_merge.ipynb
[18/42] api/18_release.ipynb
[19/42] api/02_maker.ipynb
[20/42] api/08_showdoc.ipynb
[21/42] api/09_frontmatter.ipynb
[22/42] api/03_process.ipynb
[23/42] api/05_doclinks.ipynb
[24/42] api/14_quarto.ipynb
[25/42] api/11_clean.ipynb
[26/42] api/16_migrate.ipynb
[27/42] api/15_qmd.ipynb
[28/42] api/06_sync.ipynb
[29/42] api/04_export.ipynb
[30/42] api/10_processors.ipynb
[31/42] api/13_cli.ipynb
[32/42] tutorials/qmd_intro.qmd
Starting python3 kernel...Done
Executing 'qmd_intro.ipynb'
Cell 1/1...Done
[33/42] tutorials/tutorial.ipynb
ERROR: Internal Error: Couldn't resolve width and height of SVG
```
I hope this rings a bell immediately and we don't have to dig deeper into the intimate nbdev-quarto interactions.
I'm seeing the same thing locally and also on GitHub CI, so don't think this is specific to any Linux version in particular.
Version 1.3.178 works fine.
### 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": "cscheid",
"comments": 4,
"created_at": "2023-02-09T14:31:41Z",
"creator": "xl0",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4295,
"state": "closed",
"title": "Quarto fails for `nbdev` starting with 1.3.181",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4295"
} |
### Bug description
The inline citations of literature resources sometimes, wrongly, keeps the initials or first name with the last name, for some authors, where it shouldn't. Wrong:
Right:
In my example reprex, If I change the name in the second ref (Bivand -> Bivnd), _both_ come out correctly. Also, in the example, if I remove the reference to @R-spdep in index.qmd, the rendering of the _first_ references becomes correct!
It is not as simple as a single name; this happens to multiple references (also without "and" in them) in [this book](https://github.com/edzer/sdsr); I'd be happy to share more details / examples.
Zip file:
[bug.zip](https://github.com/quarto-dev/quarto-cli/files/10697808/bug.zip)
I'm using R 4.2.2 on Ubuntu 22.04, no Rstudio, and quarto 1.2.335
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2023-02-09T13:50:32Z",
"creator": "edzer",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": null,
"number": 4294,
"state": "closed",
"title": "citations in tex sometimes keep first name or initials",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4294"
} |
### Bug description
Hi,
TOC is rendered invalid from Jupyter notebook, when raw contains HTML comment.
See:
Attaching the notebook:
(I added additional suffix *.txt, so it can be uploaded. Remove it, before testing)
[Lekcia 08 - Webove stranky a HTML.ipynb.txt](https://github.com/quarto-dev/quarto-cli/files/10696498/Lekcia.08.-.Webove.stranky.a.HTML.ipynb.txt)
| {
"assignee": null,
"comments": 1,
"created_at": "2023-02-09T11:18:25Z",
"creator": "stefansimik",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4292,
"state": "closed",
"title": "Bad TOC rendering - HTML comment",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4292"
} |
### Bug description
I would like to use "include" to generate a list with info I will use across the document.
The rendering, however, is an empty bullet.
Example:
Assume the file `warehousing_course_ilo_explain.qmd` has the content `ILO1`.
Then, the following:
```
Upon finishing the MSc Warehousing course, students will be able to:
- {{< include warehousing_course_ilo_explain.qmd >}}
{{< include warehousing_course_ilo_explain.qmd >}}
```
Results:
Upon finishing the MSc Warehousing course, students will be able to:
-
ILO1
The bug happens both in Windows and Linux (WSL) + VS Code.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-02-09T09:58:16Z",
"creator": "brenobeirigo",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 4291,
"state": "open",
"title": "Add error message when `{{< include >}}` is used in invalid position",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4291"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4265
<div type='discussions-op-text'>
<sup>Originally posted by **KaiWaldrant** February 7, 2023</sup>
We are creating a website with quarto and wanted to make use of the auto generating side bar navigation. Because we want to define the order of the layout we have added the `order` in the metadata of the `.qmd` files.
For some reason the the directory with subfolders (`contribute`) is ordered last in the navigation bar although we specified it to be higher then the `code of conduct`.
`_quarto.yaml`
```yaml
sidebar:
- id: documentation
collapse-level: 3
title: Documentation
contents: documentation
- id: neurips2021_docs
title: NeurIPS2021
contents: competitions/neurips_2021_docs
```
`documentation/code_of_conduct/index.qmd`
```yaml
---
title: Code of conduct
engine: knitr
order: 60
---
```
`documentation/contribute/index.qmd`
```yaml
---
title: Contribute
order: 4
---
```
Can anybody see what we are doing wrong or is this a bug ?
You can view a preview of the website here: [website](https://restructure-docs--openproblems-experimental.netlify.app/documentation/)
You can find the code here: [github](https://github.com/openproblems-bio/website-experimental/tree/restructure-docs)
cc @rcannood </div> | {
"assignee": null,
"comments": 3,
"created_at": "2023-02-09T09:30:12Z",
"creator": "KaiWaldrant",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4290,
"state": "closed",
"title": "auto generate ordered side navigation with subfolders",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4290"
} |
On Windows
````
> quarto --version
1.3.184
> echo 'console.log("hello")' > test.js
> quarto run test.js
WARNING: Specified QUARTO_DENO does not exist, using built in deno
hello
> $ENV:QUARTO_DENO
````
See the warning but `QUARTO_DENO` is not set on the system. Something is off.
@dragonstyle I need your help here as I don't know exactly how we are bundling the `.exe`. I know we set `QUARTO_DENO` on the `quarto.cmd` file and maybe this is still the case in the `.exe` and path is not correct ?
Logging here to not forget.
| {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2023-02-08T16:03:45Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": null,
"number": 4281,
"state": "closed",
"title": "QUARTO_DENO wrongly set internally in `quarto.exe` on Windows ? ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4281"
} |
### Bug description
Given this document:
```markdown
---
title: Example Title
format:
gfm:
markdown-headings: atx
---
# Heading
Here's some text.
## Heading 2
Here's some more text.
```
I receive the following output:
```markdown
Example Title
================
# Heading
Here’s some text.
## Heading 2
Here’s some more text.
```
Because I asked for atx-style headers, I would also like to get atx-style header for the title as well so I can then shift the heading level if needed.
Thanks!
### System info
- macOS 13.2 (22D49)
- Quarto 1.2.313
### 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": "2023-02-08T14:23:59Z",
"creator": "tomshafer",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4280,
"state": "closed",
"title": "Quarto does not render titles as atx-style H1s in Markdown",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4280"
} |
I think the CSS rules in the following lines, which are applied on website pages with the title block banned enabled, are either missing a `>` combinator or one of the `:first-of-type` should be a `:first-child` selector.
https://github.com/quarto-dev/quarto-cli/blob/0f622d36eee8b4998dbe8c17bf59abd8b229d0e1/src/resources/formats/html/templates/title-block.scss#L83-L87
What I've noticed is that the `margin-top: 0` rule is being applied to all `h2`, `h3` and `h4` that are the first in their section — so every `h3` under an `h2` anywhere on the page has top margin of zero. That doesn't seem intentional.
You can see it in Tom Mock's blog in [the _Add description and wrap_ section of this post](https://themockup.blog/posts/2022-11-08-use-r-to-generate-a-quarto-blogpost/#add-description-and-wrap) (it's the first `<h3>` under section created by an `<h2>`.
| {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2023-02-08T13:51:48Z",
"creator": "gadenbuie",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 4279,
"state": "closed",
"title": "Website title block banner heading margin applied throughout post",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4279"
} |
It appears that when I'm publishing my Jupyter notebooks to quartopub, the OG/twitter preview image urls are wrong.
Code in jupyter/qmd:
```
{.preview-image}
```
What is rendered in html:
```html
<meta property="og:image" content="https://quartopub.com/sites/ddobrinskiy/blog/posts/2023/02/nbdev_streamlit_jupyter/images/streamlit-jupyter-logo.png">
<meta name="twitter:image" content="https://quartopub.com/sites/ddobrinskiy/blog/posts/2023/02/nbdev_streamlit_jupyter/images/streamlit-jupyter-logo.png">
```
However, the [links from above](https://quartopub.com/sites/ddobrinskiy/blog/posts/2023/02/nbdev_streamlit_jupyter/images/streamlit-jupyter-logo.png) lead to 404, page not found.
The correct URL would be the following: https://ddobrinskiy.quarto.pub/blog/posts/2023/02/nbdev_streamlit_jupyter/images/streamlit-jupyter-logo.png
I'm wondering if this is a bug, or something wrong with my config?
I run `quarto publish` from the CLI to publish my website.
The source code is available here:
* quarto config: https://github.com/ddobrinskiy/blog
* jupyter notebook: https://github.com/ddobrinskiy/blog/tree/master/posts/2023/02/nbdev_streamlit_jupyter | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2023-02-08T13:28:48Z",
"creator": "ddobrinskiy",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 4278,
"state": "closed",
"title": "Wrong URL for twitter cards/open graph",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4278"
} |
### Bug description
If I am:
- working in RStudio Desktop 2023.03.0-daily+301
- in a .qmd file, in visual editor mode
- then take a windows screenshot, directed to the clipboard, and
- copy it into the visual editor window
Then, instead of getting the expected image of the screenshot, I get a broken link, such as:
By contrast, if I do this in RStudio Desktop 2022.12.1+363 the image will appear as expected.
Possibly related to #12270 and #12466.
I have seen this occur before, where in daily builds of an RStudio Desktop version, image pasting into qmd files stops working, but later it is fixed. I think it happened with Elsbeth Geranium, but if not with that, with an earlier version for sure. Because it seems like you are getting close to release of Cherry Blossom, I thought I should mention it now.
> Edition Windows 11 Pro
> Version 22H2
> Installed on 5/13/2022
> OS build 22623.1250
> Experience Windows Feature Experience Pack 1000.22639.1000.0
> platform x86_64-w64-mingw32
> arch x86_64
> os mingw32
> crt ucrt
> system x86_64, mingw32
> status
> major 4
> minor 2.2
> year 2022
> month 10
> day 31
> svn rev 83211
> language R
> version.string R version 4.2.2 (2022-10-31 ucrt)
> nickname Innocent and Trusting
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2023-02-08T13:05:16Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4277,
"state": "closed",
"title": "Cannot paste Windows screenshot into qmd file, in visual editor, in RStudio Desktop 2023.03.0-daily+301 but can in 2022.12.1+363",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4277"
} |
### Bug description
This may also affect csl (not sure)
If you use the simple book generated by `quarto create` and then switch the bibliography to an absolute path you get the following for HTML rendering:
```bash
jjallaire@jjallairesmbp2 bookwithbib % quarto render --to html
[1/4] index.qmd
[2/4] intro.qmd
[3/4] summary.qmd
[4/4] references.qmd
File Users/jjallaire/Desktop/bookwithbib/references.bib not found in resource path
ERROR: File Users/jjallaire/Desktop/bookwithbib/references.bib not found in resource path
jjallaire@jjallairesmbp2 bookwithbib %
```
Rendering docx and pdf versions of the book work as expected.
Perhaps a regression from the new book resource work for asciidoc?
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-02-08T12:57:57Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4276,
"state": "closed",
"title": "trouble rendering html books with bibliographies that use an absolute path",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4276"
} |
### Bug description
The following code yields different results for Quarto versions 1.1 and 1.3.154. In 1.1 it renders fine, caption shows and cross-referencing works. In 1.3.154 neither captioning nor cross-referencing works. Moreover, the styling of the tables is very different.
---
format: html
---
```{r}
#| include: false
library(gt)
```
```{r}
#| echo: false
#| label: tbl-mytable
#| tbl-cap: "Caption"
head(mtcars) %>% gt()
```
@tbl-mytable
It works when using `knitr::kable()` instead of `gt()` but I'm particularly interested in using `gt()` here. This issue persists on Windows 10 and Debian.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 10,
"created_at": "2023-02-08T06:29:32Z",
"creator": "snhansen",
"is_pull_request": false,
"labels": [
"bug",
"tables"
],
"locked": false,
"milestone": null,
"number": 4272,
"state": "closed",
"title": "Table caption doesn't work with gt-tables on newer Quarto versions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4272"
} |
### Bug description
After updating to 1.3.178 on Windows 10, previews of PDFs fail for my book project. See the MWE at https://github.com/fuhrmanator/quarto-test
It a git bash terminal, I usually type `quarto preview --to pdf` and it builds the PDF in `_book/book-pdf` (I think the subdir for the PDF is new?). When the viewer in the browser is opened at e.g. http://localhost:6369/web/viewer.html, there's a page with `Not Found`.
I can view the PDF with a system viewer, however, so the problem seems to be related to the browser-based previewer not finding the PDF.
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2023-02-08T05:19:18Z",
"creator": "fuhrmanator",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4271,
"state": "closed",
"title": "Quarto preview of PDF fails in Windows 1.3.178",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4271"
} |
For example:
* What version of quarto to use: dev
* To build site locally:
```
quarto render
```
* How to generate reference section (based on assumptions about location of `quarto-cli`:
```
quarto run tools/reference.ts
```
* Actions that publish website (I'm not familiar with these yet, but would be useful to document roughly when and how website is published)
| {
"assignee": "cwickham",
"comments": 5,
"created_at": "2023-02-08T01:07:22Z",
"creator": "cwickham",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4496,
"state": "open",
"title": "Add build instructions for quarto-web to README",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4496"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4266
<div type='discussions-op-text'>
<sup>Originally posted by **michiexile** February 7, 2023</sup>
I'm writing a sequence of slides using Quarto and revealjs, and want to include an index file for my slides directory - both to be able to link to it, but also because the preview defaults to `index.html`, and I want more comfortable access to each of my slides.
So my directory contains
```
index.qmd
_quarto.yml
_definitions.qmd
extra.scss
L1.qmd
L2.qmd
L3.qmd
...
```
(as well as old cruft, including a random PDF, an `.rproj` file, an `.Rhistory` file, etc)
* `_definitions.qmd` - contains a few LaTeX `\def`, and gets included early in each of the lecture files.
* `L1.qmd`, ... each starts with something like
```
---
title: "Lecture 5"
format: revealjs
---
# Point Estimation
{{< include _definitions.qmd >}}
```
* `quarto.yml`
```
project:
title: "Lectures MTH410"
render:
- "*.qmd"
- "![FS][:digit:]{2}-lectures/"
execute:
freeze: auto
author: Mikael Vejdemo-Johansson
format:
revealjs:
css: extra.css
scrollable: true
slide-number: c/t
progress: true
navigation-mode: linear
code-fold: true
error: false
warning: false
smaller: true
```
* `index.qmd`
```
---
title: "Lecture Slides and Notes"
format: html
listing:
- id: lectures
type: table
contents:
- "L[:digit:]+.qmd"
---
Here the lecture slides will appear as they are written.
::: {#lectures}
:::
```
No matter what I do, I cannot seem to get `index.qmd` to _actually_ list and link to the lecture slides themselves. `index.qmd` remains an empty page, except for the page title and whatever text I add before the div I provide for the listing itself. It doesn't matter whether I run `quarto render`, or use the Cmd-K shortcut in RStudio - same lack of results.
I don't understand why the listing does not generate. I don't understand how to get more debugging information out of quarto - trying to run preview or render with logging enabled does not give me any additional information.</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-02-07T22:51:09Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 4267,
"state": "closed",
"title": "No Listing generated (listing glob issue?)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4267"
} |
https://fluidsyndicate.com
very simple website, but using an advanced R tool for visualisation, and listing page for non-blog content.
an open source art project :) | {
"assignee": "cwickham",
"comments": 4,
"created_at": "2023-02-07T20:45:58Z",
"creator": "jcolomb",
"is_pull_request": false,
"labels": [
"documentation",
"websites"
],
"locked": false,
"milestone": null,
"number": 4506,
"state": "closed",
"title": "added another exampe to the gallery (website)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4506"
} |
Here is the issue with traceback
````
[smoke] > quarto render docs\smoke-all\2022\09\30\custom-writer-emulation\customwriter-yaml.qmd --to customformat.lua => ./test.ts:126:72
error: AssertionError: Failed assertion:
--------------------------------------------------------------------------------
[smoke] > quarto render docs\smoke-all\2022\09\30\custom-writer-emulation\customwriter-yaml.qmd --to customformat.lua
run-tests.psl ..\..\..\..\..\..\C:\Users\chris\Documents\DEV_R\quarto-cli\tests\smoke\smoke-all.test.ts
[verify] > unknown
La syntaxe du nom de fichier, de répertoire ou de volume est incorrecte. (os error 123), stat 'docs\smoke-all\2022\09\30\custom-writer-emulation\customwriter-yaml_files\figure-C:\Users\chris\Documents\DEV_R\quarto'
Error: La syntaxe du nom de fichier, de répertoire ou de volume est incorrecte. (os error 123), stat 'docs\smoke-all\2022\09\30\custom-writer-emulation\customwriter-yaml_files\figure-C:\Users\chris\Documents\DEV_R\quarto'
at Object.lstatSync (deno:runtime/js/30_fs.js:305:9)
at existsSync (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/vendor/deno.land/[email protected]/fs/exists.ts:75:10)
at removeIfEmptyDir (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/core/path.ts:47:7)
at renderCleanup (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/cleanup.ts:101:3)
at file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render.ts:293:9
at withTiming (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/core/timing.ts:37:20)
at Object.complete (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render.ts:292:7)
at async Object.onPostProcess (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:568:28)
at async renderFiles (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:524:7)
at async render (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-shared.ts:101:18)
````
We are building wrong path above `docs\smoke-all\2022\09\30\custom-writer-emulation\customwriter-yaml_files\figure-C:\Users\chris\Documents\DEV_R\quarto` by appending to path not correctly.
The issue is from
https://github.com/quarto-dev/quarto-cli/blob/104d39d2da77bdbf38cc37f33b29eb75dd23b8e7/src/command/render/cleanup.ts#L33-L36
as `format.pandoc.to` is a path. I have this in debug mode console
````
> figureFormat
'C:\Users\chris\Documents\DEV_R\quarto-cli\src\resources\filters\customwriter\customwriter.lua'
````
This leads to wrong figure directory created
https://github.com/quarto-dev/quarto-cli/blob/104d39d2da77bdbf38cc37f33b29eb75dd23b8e7/src/command/render/cleanup.ts#L96-L97
Maybe the issue is elsewhere though but here the empty directory are deleted even on Linux (no error on Linux , only windows) | {
"assignee": "cderv",
"comments": 4,
"created_at": "2023-02-07T17:00:44Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 4260,
"state": "closed",
"title": "Wrong figure folder built using custom format due to mutation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4260"
} |
This issue is here to track improvement ideas for ou tests suites
- [ ] Scheduled test on our latest build version (would help surface https://github.com/quarto-dev/quarto-cli/issues/4257 maybe)
- [ ] Testing with latest versions of R, Python and Julia packages
- [ ] Testing with dev versions of some R, Python and Julia packages
- [ ] Testing with pinned version of some know package to insure no regression (e.g for https://github.com/quarto-dev/quarto-cli/issues/4122 where jupyter-client 7 or 8 will have difference and we want to support boths)
- [ ] Improve speed of commit testing - parallelization ?
- [x] #4099 | {
"assignee": null,
"comments": 1,
"created_at": "2023-02-07T15:51:01Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 4259,
"state": "open",
"title": "Tests suite improvement ideas ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4259"
} |
### Bug description
It happens inconsistenlty, but sometimes when I preview a revealjs presentation, the Speaker View ("S") command doesn't work. If I type "?" for the list of keys, it's not available.
The solution is to save the presentation source (in VSCode) and quarto runs again. Alternatively, I can kill the preview process and re-do the preview. Again, this doesn't always fix the problem, but when it does, the "S" command is at the bottom of the help list (see below) and it works as expected:
I'm not always using `multiplex` in my presentations with students (it's useful for online, low bandwidth), but by setting `multiplex: false`, it seems to fix the behavior. I suspect it's a race condition with loading modules in the browser. Maybe the `multiplex:true` is not compatible with speakerview in preview mode? Again, I thought it worth documenting.
I'm on Windows 10, using Chrome, doing previews with `quarto preview my-presentation.qmd --to revealjs`. Quarto is version 1.3.146.
I didn't do enough tests to find the frequency, but my gut says it's like a 50% chance of happening. When I couldn't reproduce with a vanilla presentation, I found the `multiplex: true` as part of the puzzle. See the MWE at https://github.com/fuhrmanator/quarto-test/blob/d1eee4019a0af025ab325997318cf87c6586ebf8/revealjs-test/test.qmd
### 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": "cderv",
"comments": 6,
"created_at": "2023-02-07T14:48:28Z",
"creator": "fuhrmanator",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 4258,
"state": "open",
"title": "Quarto preview of revealjs sometimes doesn't have speakerview when `multiplex: true`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4258"
} |
This is the issue I get when using latest prerelease
````
cannot open C:\Users\chris\scoop\apps\quarto-prerelease\current\share\filters\customwriter\customwriter.lua: No such file or directory
````
`customwriter` folder is not in the `share` folder of my quarto installation.
This happens in the context of confluence testing
````
quarto publish confluence hello-world.qmd
````
using test repo from @allenmanning
Note: It works ok with dev version when using main branch
| {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2023-02-07T14:35:55Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4257,
"state": "closed",
"title": "customwriter.lua missing from share resource in quarto-prelease exe bundle",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4257"
} |
Test I did based on discussion below:
* Clone project https://github.com/dmbates/plotdemo which has a `_freeze` folder and use Julia.
* Delete the `docs` folder which is the output to recreate and I don't have Julia setup on my environment.
* Rendering locally with `quarto preview` -> Julia is not needed. The freezing works - HTML file is created and I can preview result
* Trying to publish using `quarto publish quarto-pub` => **Rendering using Julia is happening** - It errors on my side as not setup.
So we have an issue here I believe in our publish workflow.
Side note : Trying to publish with `--no-render` fails also
````
quarto publish quarto-pub --no-render
? Publish with account [email protected] (Y/n) » Yes
? Publish with name 'plots-demo-5bc8'? (Y/n) » Yes
[>] Creating quarto-pub document
ERROR: Output file plotdemo.html does not exist.
Error: Output file plotdemo.html does not exist.
at renderForPublish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/publish/publish.ts:235:19)
at renderForPublish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/publish/common/publish.ts:248:28)
at handlePublish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/publish/common/publish.ts:117:30)
at async publishDocument (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/publish/publish.ts:260:36)
at async publish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/publish/cmd.ts:282:9)
at async doPublish (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/publish/cmd.ts:195:7)
at async publishAction (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/publish/cmd.ts:258:7)
at async Command.fn (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/publish/cmd.ts:153:11)
at async Command.execute (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7)
at async quarto (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/quarto.ts:111:3)
````
Probably related to how the document are supposed to be rendered and why `freeze` does not work. Or another issue
cc @cscheid
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4237
<div type='discussions-op-text'>
<sup>Originally posted by **dmbates** February 5, 2023</sup>
I have been looking at the way that I currently have a Quarto book with Julia code chunks being rendered to gh-pages. (Book is at https://JuliaMixedModels.github.io/EmbraceUncertainty).
If I understand the documents at https://quarto.org/docs/publishing/github-pages.html#freezing-computations correctly then setting `freeze: auto` in `_quarto.yml` and rendering the book will save the output of the code chunks in the `_freeze` directory (which I do have committed in the repository).
I was hoping that I could then render the book in a github action without the need to configure Jupyter and a Julia kernel. However, the render and publish step fails because it can't access the kernel. (I am actually experimenting on another, private repository but can pull back the curtains if my description is too vague.)
Should this be happening or have I misconfigured the github action? In other words, is there a way I can configure the github action so that Quarto recognizes that it will use the results in the _freeze directory and can ignore the jupyter specification in the files?
An alternative approach, although perhaps less efficient, would be to get a recipe for configuring a Julia kernel in Jupyter for the github action.</div> | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-02-07T08:52:08Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"duplicate"
],
"locked": false,
"milestone": "v1.3",
"number": 4252,
"state": "closed",
"title": "Jupyter kernel needed for publish github action when freeze: auto is set",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4252"
} |
### Bug description
This code:
```r
library(rvest)
url <- "https://trace.tennessee.edu/utk_graddiss/index.html"
diss_html <- read_html(url)
diss <- diss_html %>% html_elements(".article-listing")
```
works without any problem in the R REPL or in Emacs ESS.
In Quarto, I get:
> Error in xml_ns.xml_document(x): external pointer is not valid
---
OS: Arch Linux (6.1.9-arch1-1)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 14,
"created_at": "2023-02-07T06:00:25Z",
"creator": "prosoitos",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4249,
"state": "closed",
"title": "Conflict between the rvest package and the knitr cache used by Quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4249"
} |
### Bug description
I'm getting a strange behaviour with `resources: project/wood/appfiles/` in my `quarto_yml` in recent pre-release versions (first noticed in 1.3.146 and persisting in 1.3.158). When I build my website, some of the files are not found per the output below even though the files are there per the screenshot.
If I re-install Quarto v1.2 and re-render the project, the trelliscope app re-displays again. But then re-installing the pre-release and rebuilding the site seems to lose the connection to these files and the trelliscope app no longer displays.
Version 2022.12.0+353 (2022.12.0+353)
macOS 13.2 (22D49)
```
Rendering:
[ 1/31] LICENSE.md
[ 2/31] 404.qmd
[ 3/31] about/index.qmd
[ 4/31] index.qmd
[ 5/31] blog/index.qmd
[ 6/31] blog/tail/index.qmd
Registered S3 method overwritten by 'quantmod':
method from
as.zoo.data.frame zoo
[ 7/31] blog/usedthese/index.qmd
[ 8/31] blog/dark/index.qmd
[ 9/31] blog/renovate/index.qmd
[10/31] blog/plunge/index.qmd
[11/31] project/forecast/index.qmd
[12/31] project/wood/index.qmd
[13/31] project/hansard/index.qmd
[14/31] project/forest/index.qmd
[15/31] project/un/index.qmd
[16/31] project/cetacea/index.qmd
[17/31] project/deal/index.qmd
[18/31] project/sw10/index.qmd
[19/31] project/box/index.qmd
[20/31] project/thicken/index.qmd
[21/31] project/planning/index.qmd
[22/31] project/bands/index.qmd
[23/31] project/index.qmd
[24/31] project/goldilocks/index.qmd
[25/31] project/stories/index.qmd
[26/31] project/happiness/index.qmd
[27/31] project/sets/index.qmd
[28/31] project/jitter/index.qmd
[29/31] project/six/index.qmd
[30/31] project/storm/index.qmd
Registered S3 method overwritten by 'quantmod':
method from
as.zoo.data.frame zoo
[31/31] project/footnote/index.qmd
Watching files for changes
Browse at http://localhost:7336/
GET: /
GET: /project/
GET: /project/wood/
GET: /project/wood/appfiles/index.html
/project/wood/appfiles/lib/htmlwidgets-1.6.1/htmlwidgets.js (404: Not Found)
/project/wood/appfiles/lib/trelliscopejs_widget-0.3.2/trelliscope.min.js (404: Not Found)
/project/wood/appfiles/lib/trelliscopejs_widget-binding-0.2.6/trelliscopejs_widget.js (404: Not Found)
```
But the above are there:
<img width="526" alt="Screenshot 2023-02-06 at 15 48 13" src="https://user-images.githubusercontent.com/32419319/217018209-3baab36f-46c4-4695-b5e9-ce2fa5fecd91.png">
### 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": "2023-02-06T16:25:00Z",
"creator": "cgoo4",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4245,
"state": "closed",
"title": "Strange behaviour using `resources` in recent pre-releases",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4245"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4243
<div type='discussions-op-text'>
<sup>Originally posted by **thegilpatrick** February 6, 2023</sup>
I rendered an HTML page and uploaded it on GitHub pages. Here is the [link to the webpage](https://thegilpatrick.com/blog/tidyTuesday/2023-01-31/Pet_Cats_UK.html).
The page loads fine, but none of the interactivity works on mobile (Safari or Chrome) (except for the show code button). I have some hyperlinks in markdown and you cannot click on them. I have some OJS inputs that don't work on mobile, but everything is working fine in multiple browsers (Chrome, Edge, Firefox) on desktop. I assumed at first that it was a Safari problem, but it seems to be something specific to mobile. But some of these same rendered HTML pages used to work fine on mobile before when I used a previous version of Quarto with the the `self-contained` option. I updated Quarto and now use the `embed-resources` YAML option.
Below is my YAML for the HTML page I linked. I am using Quarto version 1.2.313. I rendered this in VSCode with the extension. I have a Windows 10 Pro Operating System.
```
---
title: UK Pet Cats
subtitle: Tidy Tuesday Week 5
date: 1/31/2023
format:
html:
code-fold: true
toc: true
toc-location: left
embed-resources: true
code-tools: true
include-before-body: header.html
---
```</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-02-06T14:54:01Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 4244,
"state": "closed",
"title": "Interactivity of rendered HTML page not working on mobile browsers",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4244"
} |
### Bug description
I rendered an HTML page and uploaded it on GitHub pages. Here is the [link to the webpage](https://thegilpatrick.com/blog/tidyTuesday/2023-01-31/Pet_Cats_UK.html).
The page loads fine, but none of the interactivity works on mobile (Safari or Chrome) (except for the show code button). I have some hyperlinks in markdown and you cannot click on them. I have some OJS inputs that don't work on mobile, but everything is working fine in multiple browsers (Chrome, Edge, Firefox) on desktop. I assumed at first that it was a Safari problem, but it seems to be something specific to mobile. But some of these same rendered HTML pages used to work fine on mobile before I updated Quarto to use the new `embed-resources` YAML option.
Below is my YAML for the HTML page I linked. I rendered this in VSCode with the extension. I have a Windows 10 Pro Operating System.
```
---
title: UK Pet Cats
subtitle: Tidy Tuesday Week 5
date: 1/31/2023
format:
html:
code-fold: true
toc: true
toc-location: left
embed-resources: true
code-tools: true
include-before-body: header.html
---
```
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 0,
"created_at": "2023-02-06T14:33:39Z",
"creator": "thegilpatrick",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4242,
"state": "closed",
"title": "Rendered HTML page interactivity not working on mobile browsers",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4242"
} |
### Bug description
```
pandoc
to: latex
output-file: README.tex
standalone: true
pdf-engine: xelatex
variables:
graphics: true
tables: true
default-image-extension: pdf
metadata
documentclass: scrartcl
classoption:
- DIV=11
- numbers=noendperiod
papersize: letter
header-includes:
- '\KOMAoption{captions}{tableheading}'
block-headings: true
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999993 (TeX Live 2021) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
updating tlmgr
updating existing packages
finding package for footnote.sty
> 1 package to install
> installing mdwtools (1 of 1)
This is XeTeX, Version 3.141592653-2.6-0.999993 (TeX Live 2021) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
finding package for footnote.sty
compilation failed- package installation error
LaTeX Error: File `footnote.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Enter file name:
! Emergency stop.
<read *>
l.63 \makesavenoteenv
{longtable}^^M
see README.log for more information.
```
Fedora 37
Error is present in both RHEL tarball installations of 1.2.335 and 1.3.154. I'm pretty sure I installed the release correctly. There's no problem with HTML, only PDF.
Command:
```
quarto render README.qmd --to pdf
```
The qmd file:
```
---
format: pdf
---
# Test
Test.
```
### 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": 9,
"created_at": "2023-02-06T10:53:54Z",
"creator": "FloraCanou",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "Future",
"number": 4241,
"state": "open",
"title": "\"LaTeX Error: File `footnote.sty' not found\" on output to PDF",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4241"
} |
### Bug description
Some RevealJS themes (beige, league, sky) don't support animation of code line number highlighting per https://quarto.org/docs/presentations/revealjs/#line-highlighting (see the example where one can advance with space-bar to show highlighted lines). In the faulty themes, it seems the "background" code is not properly grayed out (so the highlighted code appears to stand out).
Here's a MWE for the problem:
````md
---
format:
revealjs:
theme: beige # doesn't work
# theme: blood # works
# theme: dark # works
# theme: default # works
# theme: league # doesn't work
# theme: moon # works
# theme: night # works
# theme: serif # works
# theme: simple # works
# theme: sky # doesn't work
# theme: solarized # works
---
# Animated slide
```{.python code-line-numbers="|6|9"}
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()
```
````
This could very well be a bug in the highlight.js or even the CSS of the themes. I didn't have time to dig deeper, but wanted to document it.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 2,
"created_at": "2023-02-05T17:34:25Z",
"creator": "fuhrmanator",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 4233,
"state": "open",
"title": "RevealJS code block animations not working on several themes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4233"
} |
### Bug description
I have been copying and running the same qmd file week in and week out. This week when I ran it, it printed:
::: panel tabset
:::
Instead of creating tabs it worked only as headers, but when I threw in some dummy tabs elsewhere in the document, tabs were created, ie.
::: panel tabset
## does
this
## work
oh
## my
it did
:::
The website I have been populating is:
https://racing-focus.netlify.app/posts/hk_2023-02-01/standard.html
If you look at the posts, todays post I reverted to a table of contents style post with conventional headers.
I tried to drag and drop the qmd files, but that failed so I renamed them .txt. The file I used today and the previous ones that worked. I am not a 'good' programmer and apologise for the code you will see.
The qmd file relies on a couple of csv files which I have added too.
I am using the following version of rstudio and I have been for a little while now.
RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 11_5_2) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
I am using a Mac. I don't have a bug report, because it works, it just prints ::: panel tabset.
I googled for an answer and couldn't find one or one on here. Thanks and Sorry.
[standard_prev.txt](https://github.com/quarto-dev/quarto-cli/files/10610738/standard_prev.txt)
[standard_today
[hkedit.csv](https://github.com/quarto-dev/quarto-cli/files/10610744/hkedit.csv)
[red.csv](https://github.com/quarto-dev/quarto-cli/files/10610742/red.csv)
.txt](https://github.com/quarto-dev/quarto-cli/files/10610739/standard_today.txt)
### 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": "2023-02-05T10:57:50Z",
"creator": "racing-focus",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4230,
"state": "closed",
"title": "Quarto - Panel Tabset",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4230"
} |
It might make sense for us to leverage cell magics to support (eg) a native `sql` cell in the same way that knitr does it.
Pros:
- it's a popular request
- it would us get closer to matching the behavior in the `knitr` engine
Cons:
- it would make it even harder for beginners to reason about what engine is responsible for what execution. Specifically, cell magics are specific to the ipython kernel
- it would not solve the problem for _other_ jupyter kernels
If we continue to increase the ways in which different engines interpret `{language}` cells, I think it would be a good idea for quarto to be able to `explain` who runs what cells. I can imagine a TypeScript API that could do so.
| {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-02-04T20:09:40Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"jupyter"
],
"locked": false,
"milestone": "v1.4",
"number": 4227,
"state": "open",
"title": "SQL cell (and others?) in jupyter engine and ipython kernel",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4227"
} |
### Bug description
Compiling a qmd file to PDF doesn't work if it contains an R HTML widget. Here is a minimal reproducible example with a leaflet map (but the behavior is the same with a visNetwork graph for example) :
````md
---
format:
pdf:
prefer-html: false
---
# Leaflet test
```{r}
library(leaflet)
leaflet() %>%
addTiles()
```
````
When rendering to PDF with `prefer-html: false`, I get the following error message :
> 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 of
your quarto file:
>
> prefer-html: true
>
> Note however that the HTML output will not be visible in non-HTML formats.
If I set `prefer-html: true`, I get another error message during xelatex compilation step :
> compilation failed- error
> LaTeX Error: Missing \begin{document}.
>
> See the LaTeX manual or LaTeX Companion for explanation.
> Type H <return> for immediate help.
> ...
>
> l.141 <
> script src="site_libs/htmlwidgets-1.6.1/htmlwidgets.js"></script>
Indeed, if I take a look at the generated TeX file there are `<script>` and `<link>` tags inserted inside TeX code.
I'm using quarto 1.2.335 with Visual Studio code under Linux (KDE Neon / Ubuntu 22.04).
Thanks a lot !
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 4,
"created_at": "2023-02-04T19:18:23Z",
"creator": "juba",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4225,
"state": "open",
"title": "Can't compile to PDF when including an R HTML widget",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4225"
} |
### Bug description
_No response_
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2023-02-04T18:40:54Z",
"creator": "mroberts1",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4224,
"state": "closed",
"title": "Other formats not posting in margin",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4224"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4217
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** February 4, 2023</sup>
Hi,
I would like to add a paginated html simple table in a quarto HTML output.
I was thinking of using [itables](https://mwouts.github.io/itables/quick_start.html), because it works very well in my jupyter notebook and it's very simple to use.
The code is this
~~~~
```{python}
#| echo: false
from itables import init_notebook_mode
init_notebook_mode(connected=True)
init_notebook_mode(all_interactive=True)
from itables.sample_dfs import get_countries
df = get_countries()
df
```
~~~~
But it remains in loading status
It seems that [it's necessary to load a trusted notebook](https://mwouts.github.io/itables/troubleshooting.html). Is there a way to pass "trusted" status via quarto code?
Thank you</div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2023-02-04T17:35:14Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"jupyter"
],
"locked": false,
"milestone": "v1.4",
"number": 4223,
"state": "open",
"title": "\"trusted notebook execution\"",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4223"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4220
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** February 4, 2023</sup>
Hi,
I have read the documentation, and this should work
~~~~
```{python}
#| echo: false
#| label: tbl-ref
#| tbl-cap: "Main Caption"
import pandas as pd
from IPython.display import display
df = pd.read_csv("../../data/anac/tmp_cup_anac.csv", sep=",")
table=df.head(3).style. Hide(axis='index')
display(table)
```
~~~~
But I have no caption table.
I'm using 1.3.142 version on Debian 11.
Thank you
</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2023-02-04T17:30:59Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"tables"
],
"locked": false,
"milestone": "v1.3",
"number": 4222,
"state": "closed",
"title": "How to render in python table caption, for html output?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4222"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4216
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** February 4, 2023</sup>
Hi,
I have the below sample code.
~~~~
```{ojs}
//| echo: false
//| column: page
data = FileAttachment("input.csv").csv({ typed: true })
Inputs.table(data)
```
~~~~
I would like to apply [Page Column](https://quarto.org/docs/authoring/article-layout.html#page-column), but it seems not work for observable.
Thank you</div> | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2023-02-04T17:29:35Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "v1.4",
"number": 4221,
"state": "open",
"title": "Observable and article layout: is it possible to use it?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4221"
} |
### Bug description
_No response_
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2023-02-04T13:48:44Z",
"creator": "mroberts1",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4218,
"state": "closed",
"title": "Other Formats links not appearing in margin",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4218"
} |
### Bug description
I'd like to ask if there are any plans to support arm64 for Linux?
Quarto not being available for arm64 currently blocks a full-fledged Posit Workbench arm64 setup.
AFAICS one blocking issue is that `deno` is not yet available for arm64? https://github.com/denoland/deno/issues/1846
### 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": 17,
"created_at": "2023-02-04T11:47:02Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [
"bug",
"early-in-release"
],
"locked": false,
"milestone": "v1.4",
"number": 4215,
"state": "closed",
"title": "Support for arm64 arch",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4215"
} |
### Bug description
I'm testing the new code annotations feature in Quarto pre-release 1.3.154 (MacOS; RStudio IDE Version 2022.12.0+353 (2022.12.0+353)) in a Reveal JS presentation.
When using the `output-location: slide` option, the annotations appear on the output slide rather than on the slide associated with code.
Here's a reprex:
````
---
title: "reprex"
format: revealjs
---
## Code with annotation
```{r}
#| echo: true
#| output-location: slide
x <- seq(-2*pi, 2*pi, by=pi/100) # <1>
y <- sin(x) # <2>
plot(x, y, type = "l")
```
1. Annotation 1
2. Annotation 2
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-02-04T01:03:59Z",
"creator": "pmagwene",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4213,
"state": "closed",
"title": "Code annotations don't work well with `output-location: slide`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4213"
} |
### Bug description
Environment: Arch Linux
Deno: 1.30.1
RStudio vesion: irrelevant
AUR Package: quarto-cli-pre-release (I'm maintainer)
Since 1.29 Deno has dropped some API calls, in particular, `Deno.spawnSync`. As result the following error has thrown when I'm trying to build `quarto-cli-pre-release`:
```
Creating Deno Bundle
/var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/package/dist/bin/quarto.js
Check file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/src/quarto.ts
error: TS2339 [ERROR]: Property 'spawnSync' does not exist on type 'typeof Deno'.
Deno.spawnSync;
~~~~~~~~~
at file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/src/vendor/deno.land/[email protected]/node/process.ts:63:8
TS2367 [ERROR]: This comparison appears to be unintentional because the types 'rmdirOptions | undefined' and 'boolean' have no overlap.
if (options === false) {
~~~~~~~~~~~~~~~~~
at file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/src/vendor/deno.land/[email protected]/node/_fs/_fs_rmdir.ts:88:9
Found 2 errors.
ERROR: Failure to bundle /var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/src/quarto.ts
Error: Failure to bundle /var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/src/quarto.ts
at bundle (file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/package/src/util/deno.ts:40:11)
at async prepareDist (file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/package/src/common/prepare-dist.ts:39:3)
at async Command.fn (file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/package/src/cmd/pkg-cmd.ts:38:5)
at async Command.execute (https://deno.land/x/[email protected]/command/command.ts:1790:7)
at async quartoBld (file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/package/src/bld.ts:48:3)
at async mainRunner (file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/src/core/main.ts:39:5)
at async file:///var/tmp/makepkg/quarto-cli-pre-release/src/quarto-cli-1.3.154/package/src/bld.ts:52:3
==> ERROR: A failure occurred in build().
Aborting...
```
I hope upgrade of https://github.com/quarto-dev/quarto-cli/tree/main/src/vendor/deno.land/std%400.166.0 to the most recent version (https://github.com/denoland/deno_std/releases/tag/0.176.0) might resolve the issue....
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2023-02-03T21:14:35Z",
"creator": "trap000d",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4212,
"state": "closed",
"title": "Won't build with Deno >=1.29 ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4212"
} |
### Bug description
With quarto version 1.2.335, I tried to use `keep-yaml` to preserve the yaml frontmatter in quarto outputs. This does not work for markdown formats such as `gfm` and `commonmark`.
``` r
frontmatter <- paste0(readLines("frontmatter"), collapse = "\n")
cat(frontmatter)
#> ---
#> title: hello world
#> author: jane doe
#> draft: true
#> format:
#> gfm:
#> keep-yaml: true
#> ---
file.create("test.qmd")
#> [1] TRUE
cat(frontmatter, file = "test.qmd")
quarto::quarto_render("test.qmd")
#> [1mpandoc [22m
#> to: >-
#> commonmark+autolink_bare_uris+emoji+footnotes+gfm_auto_identifiers+pipe_tables+strikeout+task_lists+tex_math_dollars
#> output-file: test.md
#> standalone: true
#> default-image-extension: png
#>
#> [1mmetadata[22m
#> title: hello world
#> author: jane doe
#> draft: true
#> keep-yaml: true
#>
#> Output created: test.md
readLines("test.md")
#> [1] "hello world" "================" "jane doe" ""
```
<sup>Created on 2023-02-03 with [reprex v2.0.2](https://reprex.tidyverse.org)</sup>
### 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": 14,
"created_at": "2023-02-03T19:34:34Z",
"creator": "qiushiyan",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4210,
"state": "open",
"title": "`keep-yaml` not working for markdown formats",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4210"
} |
### Bug description
I'm having issues rendering the shinylive example document described [here](https://github.com/quarto-ext/shinylive). I followed the instructions for installing the extension which seemed successful. However, when I try to render the following example document:
```
---
title: Shinylive in Quarto example
format: html
filters:
- shinylive
---
This is a Shinylive application embedded in a Quarto doc.
```{shinylive-python}
#| standalone: true
from shiny import *
app_ui = ui.page_fluid(
ui.input_slider("n", "N", 0, 100, 40),
ui.output_text_verbatim("txt"),
)
def server(input, output, session):
@output
@render.text
def txt():
return f"The value of n*2 is {input.n() * 2}"
app = App(app_ui, server)
```
it results in an error:
```
pandoc
to: html
output-file: test.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: Shinylive in Quarto example
Error running filter C:/Users/au234616/AppData/Local/Programs/Quarto/share/filters/main.lua:
PandocLuaError "PandocFilterError \"D:\\\\quartotest\\\\shinylive\\\\shinylive\" \"Could not find executable D:\\\\quartotest\\\\shinylive\\\\shinylive\"\nstack traceback:\n\t...616/AppData/Local/Programs/Quarto/share/filters/main.lua:3911: in function <...616/AppData/Local/Programs/Quarto/share/filters/main.lua:3891>\n\t[C]: in ?\n\t[C]: in method 'walk'\n\t...616/AppData/Local/Programs/Quarto/share/filters/main.lua:153: in function 'run_emulated_filter'\n\t...616/AppData/Local/Programs/Quarto/share/filters/main.lua:403: in local 'callback'\n\t...616/AppData/Local/Programs/Quarto/share/filters/main.lua:408: in upvalue 'run_emulated_filter_chain'\n\t...616/AppData/Local/Programs/Quarto/share/filters/main.lua:443: in function <...616/AppData/Local/Programs/Quarto/share/filters/main.lua:424>"
stack traceback:
...616/AppData/Local/Programs/Quarto/share/filters/main.lua:153: in function 'run_emulated_filter'
...616/AppData/Local/Programs/Quarto/share/filters/main.lua:403: in local 'callback'
...616/AppData/Local/Programs/Quarto/share/filters/main.lua:408: in upvalue 'run_emulated_filter_chain'
...616/AppData/Local/Programs/Quarto/share/filters/main.lua:443: in function <...616/AppData/Local/Programs/Quarto/share/filters/main.lua:424>
```
This is on Windows 10 using Quarto v. 1.3.142
Here's the result of `quarto check`:
```
[>] Checking versions of quarto binary dependencies...
Pandoc version 2.19.2: OK
Dart Sass version 1.32.8: OK
[>] Checking versions of quarto dependencies......OK
[>] Checking Quarto installation......OK
Version: 1.3.142
Path: C:\Users\au234616\AppData\Local\Programs\Quarto\bin
CodePage: unknown
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.11.1
Path: C:/Users/au234616/AppData/Local/Programs/Python/Python311/python.exe
Jupyter: 5.2.0
Kernels: python3
(/) Checking Jupyter engine render....0.01s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.2.1
Path: C:/PROGRA~1/R/R-42~1.1
LibPaths:
- C:/Users/au234616/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.1/library
rmarkdown: 2.17
[>] 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": null,
"comments": 1,
"created_at": "2023-02-03T17:17:11Z",
"creator": "snhansen",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4207,
"state": "closed",
"title": "Error rendering document with the shinylive extension",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4207"
} |
### Bug description
Currently when an `error` is rendered in the output, the ascii escape codes are also printed out
This is what it looks like in the terminal:
It would be nice if either quarto
1) starts julia with the flag `--color=no`. This is the same output in the terminal with that flag
OR
2) parses ascii codes in outputs using a javascript library to generate color html output. For example, you could vendor this: https://github.com/drudru/ansi_up
Reproducible example:
Create a `_quarto.yml` file:
```
project:
type: website
title: "MethodError"
output-dir: _output
execute-dir: project
execute:
output: true
echo: true
warning: true
error: true
freeze: auto
eval: true
cache: true
jupyter: julia-1.8
```
Create a `index.qmd` file:
````md
---
title: Method error
---
#### MethodError
```{julia}
ceil(1.2 + 2.3im)
```
````
Version information:
```julia
julia> versioninfo()
Julia Version 1.8.5
Commit 17cfb8e65e (2023-01-08 06:45 UTC)
Platform Info:
OS: Windows (x86_64-w64-mingw32)
CPU: 8 × 11th Gen Intel(R) Core(TM) i5-1145G7 @ 2.60GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-13.0.1 (ORCJIT, tigerlake)
Threads: 1 on 8 virtual cores
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-02-03T13:01:45Z",
"creator": "kdheepak",
"is_pull_request": false,
"labels": [
"bug",
"julia",
"triaged-to"
],
"locked": false,
"milestone": "v1.4",
"number": 4204,
"state": "open",
"title": "When an error is rendered in the output, the ascii escape codes should be stripped or processed to HTML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4204"
} |
### Bug description
I'm getting an error when trying to install the `parse-latex` extension available [here](https://github.com/tarleb/parse-latex).
Here is the error message from running `quarto install extension tarleb/parse-latex`:
```
Quarto extensions may execute code when documents are rendered. If you do not
trust the authors of the extension, we recommend that you do not install or
use the extension.
? Do you trust the authors of this extension (Y/n) » Yes
[>] Downloading
parse-latex-main/parse-latex.lua: Can't create '\\\\?\\C:\\Users\\au234616\\AppData\\Local\\Temp\\quarto-sessionb2f134f6\\4905fc74\\a45d7e9e\\archive\\parse-latex-main\\parse-latex.lua'
tar: Error exit delayed from previous errors.
[>] Unzipping
ERROR: Failed to unzip extension.
parse-latex-main/parse-latex.lua: Can't create '\\\\?\\C:\\Users\\au234616\\AppData\\Local\\Temp\\quarto-sessionb2f134f6\\4905fc74\\a45d7e9e\\archive\\parse-latex-main\\parse-latex.lua'
tar: Error exit delayed from previous errors.
```
This is running Quarto 1.3.142 on Windows 10. Any ideas what's causing this error?
### 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": 16,
"created_at": "2023-02-03T12:57:07Z",
"creator": "snhansen",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 4203,
"state": "closed",
"title": "Error installing Quarto extension",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4203"
} |
### Bug description
[`code-filename`](https://quarto.org/docs/output-formats/html-code.html#code-filename) is not working for latest pre-release [version 1.3.151](https://quarto.org/docs/download/prerelease.html) for pdf output format but works for html format. But `code-filename` was working for both formats in previous versions.
### `format: html` (Works!)
~~~
---
title: "Untitled"
format: html
---
## filename
```{.python filename="matplotlib.py"}
import matplotlib.pyplot as plt
plt.plot([1,23,2,4])
plt.show()
```
~~~
### `format: pdf` (Doesn't Work!)
~~~
---
title: "Untitled"
format: pdf
---
## filename
```{.python filename="matplotlib.py"}
import matplotlib.pyplot as plt
plt.plot([1,23,2,4])
plt.show()
```
~~~
And getting this error (from quarto's internal lua filter)
> Error running filter C:/Users/User/AppData/Local/Programs/Quarto/share/filters/main.lua:
PandocLuaError "...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:3369: bad argument `#1` to 'insert' (table expected, got nil)\nstack traceback:\n\t...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:3369: in function 'tprepend'\n\t...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:14710: in function <...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:14659>\n\t(...tail calls...)\n\t...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:67: in function 'process_custom'\n\t(...tail calls...)\n\t[C]: in ?\n\t[C]: in method 'walk'\n\t...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:153: in function 'run_emulated_filter'\n\t...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:405: in local 'callback'\n\t...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:410: in upvalue 'run_emulated_filter_chain'\n\t...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:451: in function <...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:432>"
stack traceback:
...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:153: in function 'run_emulated_filter'
...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:405: in local 'callback'
...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:410: in upvalue 'run_emulated_filter_chain'
...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:451: in function <...ser/AppData/Local/Programs/Quarto/share/filters/main.lua:432>
I am running Quarto from **RStudio 2022.07.2+576 "Spotted Wakerobin"** and using **windows 10**.
~~~
> xfun::session_info()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044), RStudio 2022.7.2.576
~~~
~~~
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": 2,
"created_at": "2023-02-03T11:18:11Z",
"creator": "shafayetShafee",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4200,
"state": "closed",
"title": "code filename is not working for pre-release Quarto version 1.3.151 for pdf format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4200"
} |
Some part of v8's startup process mmaps an 8GB chunk of memory. We need to allow users to configure that. | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2023-02-03T00:51:49Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4197,
"state": "open",
"title": "limited environments run into deno memory issues",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4197"
} |
### Bug description
Code annotations disable the "copy code" button.
````
---
format: html
---
Code without annotation - has code copy button on hover:
```r
1 + 1
```
Code with annotation - no code copy button:
```r
1 + 1 # <1>
```
1. Arithmetic
````
I think it makes sense for the copy to exclude the annotation. So "copying" second chunk should give just contents of the first chunk:
```r
1 + 1
```
Dev Quarto, Mac OS, RStudio Version 2022.12.0+353 (2022.12.0+353)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2023-02-02T19:53:08Z",
"creator": "cwickham",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 4196,
"state": "closed",
"title": "Code annotation disables copy code button",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4196"
} |
### Bug description
From #3847, it seems like it should be possible to use fenced divs to indicate that a section of Markdown in .qmd should be converted into two separate Markdown cells in Jupyter, but this does not seem to be the case.
Tested on Quarto v1.2.335, on both Arch Linux and Ubuntu 22.04.
Here is a sample file `simple.qmd`:
```markdown
---
title: Simple version
---
# Lorem ipsum
**Lorem ipsum** dolor sit amet, consectetur adipiscing elit. Nunc luctus
bibendum felis dictum sodales.
:::::: {.cell .markdown}
# Lorem ipsum
**Lorem ipsum** dolor sit amet, consectetur adipiscing elit. Nunc luctus
bibendum felis dictum sodales.
::::::
```
Expected Jupyter notebook after running `quarto convert simple.qmd`:
```json
{
"cells": [
{
"cell_type": "raw",
"metadata": {},
"source": [
"---\n",
"title: Simple version\n",
"---"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Lorem ipsum\n",
"\n",
"**Lorem ipsum** dolor sit amet, consectetur adipiscing elit. Nunc luctus\n",
"bibendum felis dictum sodales.\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"\n",
"# Lorem ipsum\n",
"\n",
"**Lorem ipsum** dolor sit amet, consectetur adipiscing elit. Nunc luctus\n",
"bibendum felis dictum sodales."
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
```
Actual Jupyter notebook output (`simple.ipynb`):
```json
{
"cells": [
{
"cell_type": "raw",
"metadata": {},
"source": [
"---\n",
"title: Simple version\n",
"---"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Lorem ipsum\n",
"\n",
"**Lorem ipsum** dolor sit amet, consectetur adipiscing elit. Nunc luctus\n",
"bibendum felis dictum sodales.\n",
"\n",
":::::: {.cell .markdown}\n",
"# Lorem ipsum\n",
"\n",
"**Lorem ipsum** dolor sit amet, consectetur adipiscing elit. Nunc luctus\n",
"bibendum felis dictum sodales.\n",
"::::::"
]
}
],
"metadata": {
"kernelspec": {
"name": "python3",
"language": "python",
"display_name": "Python 3 (ipykernel)"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
```
As a side note, the command mentioned in #3847 (`quarto convert simple.qmd --to ipynb`) does not work, and the `--to` option does not appear in the output of `quarto help convert`. It may be that there's another setup step or command flag that I've missed, but I couldn't seem to find a fix.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2023-02-02T19:21:33Z",
"creator": "syclops",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4195,
"state": "closed",
"title": "Cannot generate separate Markdown cells in Jupyter",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4195"
} |
Test error
````
[smoke] > quarto render docs\project\site -o - => ./test.ts:121:72
error: AssertionError: Failed assertion:
--------------------------------------------------------------------------------
[smoke] > quarto render docs\project\site -o -
run-tests.psl ..\..\..\..\..\..\C:\Users\chris\Documents\DEV_R\quarto-cli\tests\smoke\project\project-stdout.test.ts
[verify] > unknown
La syntaxe du nom de fichier, de répertoire ou de volume est incorrecte. (os error 123), stat 'C:\Users\chris\Documents\DEV_R\quarto-cli\tests\docs\project\site\C:\Users\chris\AppData\Local\Temp\quarto-session96c8468e\9b1cbc71\dc6b9af2_files'
Error: La syntaxe du nom de fichier, de répertoire ou de volume est incorrecte. (os error 123), stat 'C:\Users\chris\Documents\DEV_R\quarto-cli\tests\docs\project\site\C:\Users\chris\AppData\Local\Temp\quarto-session96c8468e\9b1cbc71\dc6b9af2_files'
at Object.lstatSync (deno:runtime/js/30_fs.js:305:9)
at existsSync (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/vendor/deno.land/[email protected]/fs/exists.ts:75:10)
at removeIfEmptyDir (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/core/path.ts:47:7)
at renderProject (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/project.ts:347:9)
at async Command.fn (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/cmd.ts:193:26)
at async Command.execute (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/vendor/deno.land/x/[email protected]/command/command.ts:1790:7)
at async quarto (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/quarto.ts:111:3)
at async Object.execute (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/tests/test.ts:68:5)
at async fn (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/tests/test.ts:165:11)
at async Object.testStepSanitizer [as fn] (deno:cli/js/40_testing.js:448:7)
````
That is definitely not correctly build
````
C:\Users\chris\Documents\DEV_R\quarto-cli\tests\docs\project\site\C:\Users\chris\AppData\Local\Temp\quarto-session96c8468e\9b1cbc71\dc6b9af2_files
````
It comes from
https://github.com/quarto-dev/quarto-cli/blob/9ce89221b1ac4f36a0826c8a9778b9e60b045f66/src/command/render/project.ts#L305-L312
If I had some log info
````
if (!keepFiles) {
console.log(projDir);
console.log(renderedFile.file);
console.log(dirname(renderedFile.file));
console.log(inputFilesDir(renderedFile.file));
````
this is the result
````
C:\Users\chris\Documents\DEV_R\quarto-cli\tests\docs\project\site
C:\Users\chris\AppData\Local\Temp\quarto-session96c8468e\9b1cbc71\dc6b9af2.html
C:\Users\chris\AppData\Local\Temp\quarto-session96c8468e\9b1cbc71
dc6b9af2_files
````
Definitely not right
| {
"assignee": "cscheid",
"comments": 4,
"created_at": "2023-02-02T18:15:57Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 4194,
"state": "open",
"title": "Removing empty dir is not working as wrong path is created (when outputing to stdout)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4194"
} |
Opening this to think about it further. See discussion
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/4182
<div type='discussions-op-text'>
<sup>Originally posted by **sagikazarmark** February 1, 2023</sup>
I want to include a certain piece of CSS in all of my slides (regardless of the theme), but still want to be able to use custom CSS on a per slide basis if I want to.
Currently if I set a default value for `theme` with a custom css file, it gets overridden as soon as I pick another theme in a slide (which is kind of expected).
I'd like to be able to include a CSS file in addition to the theme.
A good enough workaround for now is using `include-in-header`, but that can still be overridden.</div>
(More details shared later)
Here is what I have in my `_quarto.yml` file:
```yaml
format:
revealjs:
theme: [default, custom.scss]
```
Then in any slide, if I want to use another theme:
```markdown
---
format:
revealjs:
theme: sky
---
```
I want to be able to include my `custom.scss` in all of my slides without having to remember to include it when I don't use the default value.
What I'm currently doing is I have `include-in-header` defined in my `_quarto.yml` to include custom CSS. I don't use `include-in-header` at the moment anywhere in my slides which is why I can rely on the default. | {
"assignee": "cderv",
"comments": 4,
"created_at": "2023-02-02T17:28:53Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 4193,
"state": "open",
"title": "[revealjs] Global custom theme configuration that is not override locally",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4193"
} |
### Bug description
TLDR: When using a custom Julia system image in a project, the first format renders fine, but subsequent try to use a different kernel w/o the system image. This works locally but not in CI. I *think* it may be due to daemon handling without TTY.
I have a project using Julia with a custom system image. I built an IJulia kernel called `julia-sysimage-1.8` that uses a system image located at `/precompiled.so`
My _quart.yml looks like
```yaml
project:
title: "My Project"
jupyter: julia-sysimage-1.8
format:
elsevier-pdf:
latex-clean: false
keep-tex: true
elsevier-html:
toc: true
embed-resources: true
```
I write and render this project on my local machine inside a devcontainer specified as below. Where the image contains the system image, jupyter, ...
```json
{
"name": "Quarto",
"image": "MY_CUSTOM_IMAGE",
"customizations": {
"vscode": {
"extensions": [
"julialang.language-julia",
"quarto.quarto"
],
"settings": {
"julia.additionalArgs": ["--sysimage=/precompiled.so"],
"quarto.render.renderOnSave": false
}
}
},
// due to https://github.com/quarto-dev/quarto-cli/issues/4122
"postCreateCommand": "pip install --force-reinstall jupyter-client==7.4.9 && \
julia --sysimage=/precompiled.so --project=@. -e \"using Pkg; Pkg.instantiate()\"",
"features": {
"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
// "version": "prerelease",
"version": "latest",
"installTinyTex": true,
"installChromium": false
}
}
}
```
Running `quarto render` from VSCode w/ the devcontainer works perfectly fine. HOWEVER, in CI I render using Docker-in-Docker via
```
- devcontainer up --workspace-folder .
- devcontainer exec --workspace-folder . quarto render papers/quarto --execute-daemon --output-dir ../../public
```
Building the container and rendering the pdf target takes about ~6min total both locally and in CI. However, the html target takes an additional 16 min in CI. Both renders show `Starting julia-sysimage-1.8 kernel...`.
Adding
````markdown
```{julia}
#| echo: true
versioninfo()
```
```{julia}
#| echo: false
println("Sysimage: $(unsafe_string(Base.JLOptions().image_file))")
```
````
shows that the first render target (pdf) uses the correct system image, while the second does not (wrong system image), despite printing `Starting julia-sysimage-1.8 kernel...` to stdout for both. Also using `--execute-daemon` when inside the devcontainer only starts a single kernel but two separate ones are started in the CI setup. The docs mention
> Accordingly, no daemon is created when documents are rendered without an active tty
which is what leads me to believe that tty handling may be the issue.
PDF:
<img width="737" alt="Screen Shot 2023-02-02 at 10 58 30 AM" src="https://user-images.githubusercontent.com/599421/216388613-6e377a89-d982-4e14-bc88-50a36cd344dc.png">
HTML:
<img width="823" alt="Screen Shot 2023-02-02 at 10 58 17 AM" src="https://user-images.githubusercontent.com/599421/216388710-278cf7ec-fde3-4762-96fa-bfdea444568e.png">
I realize that this a complex example. I could provide a minimal setup but that would still require somebody to compile a custom system image which is non-trivial. Thanks.
Local machine : OSX w/ Debian 11-based devcontainer
CI Runner: Debian 11 -> docker:latest -> same devcontainer as local machine.
### 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": "2023-02-02T17:11:45Z",
"creator": "agerlach",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4192,
"state": "closed",
"title": "Projects w/ multiple output formats uses different kernels per render",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4192"
} |
### Bug description
Speaker notes print in pdf output. They are appropriately hidden in html output. This illustrates the issue:
````
---
title: Test
format: pdf
---
# A section head
Some text
::: {.notes}
Hidden speaker notes
:::
````
Attached are a qmd file and output:
[quarto-issue-speaker-notes.zip](https://github.com/quarto-dev/quarto-cli/files/10564504/quarto-issue-speaker-notes.zip)
This is using quarto version 1.3.146 (also occurred in earlier 1.3 versions) under Ubuntu 22.04.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2023-02-02T03:35:45Z",
"creator": "rmcd1024",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 4189,
"state": "closed",
"title": "Speaker notes are printed in pdf output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4189"
} |
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