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|---|---|
### Bug description
```
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: 1.3.97
Path: C:\Program Files\Quarto\bin
CodePage: 1252
[>] Checking basic markdown render....OK
ERROR: SyntaxError: Unexpected token '', ""... is not valid JSON
```
This error appeared suddenly after rebooting my computer...
### 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": 8,
"created_at": "2023-01-11T22:55:36Z",
"creator": "vaulot",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3936,
"state": "closed",
"title": "ERROR: SyntaxError: Unexpected token '', \"\"... is not valid JSON when doing quarto check",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3936"
}
|
See https://github.com/quarto-dev/quarto-r/issues/73#issuecomment-1379244465
|
{
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2023-01-11T18:08:03Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 3933,
"state": "open",
"title": "theme / highlighting CSS appears in cases it seems it shouldn't",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3933"
}
|
Hi,
Is there a way to obtain a numbered table caption above a single table using div elements: ":::"?
According to the documentation at [tables ](https://quarto.org/docs/authoring/tables.html) one can use div elements around multiple tables to get a a **numbered table** with the caption above using this code:
For example, this code:
````
::: {#tbl-panel layout-ncol=2}
| Col1 | Col2 | Col3 |
|------|------|------|
| A | B | C |
| E | F | G |
| A | G | G |
: First Table {#tbl-first}
| Col1 | Col2 | Col3 |
|------|------|------|
| A | B | C |
| E | F | G |
| A | G | G |
: Second Table {#tbl-second}
Main Caption
:::
````
will give a numbered table with caption above as I want. But when using a single table, the table number is not displayed, like this code:
````
::: {#tbl-panel}
| Col1 | Col2 | Col3 |
|------|------|------|
| A | B | C |
| E | F | G |
| A | G | G |
Main Caption
:::
````
I am trying to use this as a workaround to get numbered table caption above my datatable produced using R. In the following code, I would like the table caption to be numbered according to the order it appears in the document (relative to other tables), and appear above the datatable.
````
::: {#tbl-panel}
```{r}
library(DT)
datatable(my_interactive_table)
```
My table caption that should give the table number and appear above the table.
:::
````
Thank you for your time and help,
Magnus NygΓ₯rd Osnes
|
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-01-11T09:44:45Z",
"creator": "magnusnosnes",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 3931,
"state": "open",
"title": "Table number does not appear when using a single table inside a div element.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3931"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3918
<div type='discussions-op-text'>
<sup>Originally posted by **ThierryO** January 10, 2023</sup>
With version 1.1.189 we could add custom variables to the book settings in `_quarto.yml` and use them in the template. The example below provided `$book.reportnr$` in the template.
```
book:
title: my title
reportnr: 99999
```
After upgrading to version 1.2.313 this results in an error `property name reportnr is invalid`. How can we pass custom variables to a template in an extension?</div>
|
{
"assignee": "cscheid",
"comments": 0,
"created_at": "2023-01-10T15:40:05Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"documentation",
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3919,
"state": "open",
"title": "Specify which portions of the YAML namespace are safe for extensions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3919"
}
|
This comes from https://github.com/quarto-dev/quarto-r/issues/22
R users have such feature with `blogdown::new_post()` and a RStudio Addin build upon it. I believe it would be a nice feature to have in our `quarto create ...` suites of features.
This would help
* Create a post in the right place in the Quarto blog
* Add some content to the file based on a default or template maybe
* Offer to fill some fields at command line maybe like title, etc...
|
{
"assignee": null,
"comments": 7,
"created_at": "2023-01-10T14:46:11Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3917,
"state": "open",
"title": "[FR]: Easily add a new post in a blog e.g `quarto create post` ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3917"
}
|
Hi!
When using Rstudio, Quarto is installed locally, the option to use the Quarto preview/in general the whole Global options Quarto tab is missing, is this intentional?
Thanks a lot for checking.
compare this with the instructions given at https://quarto.org/docs/tools/rstudio.html
|
{
"assignee": null,
"comments": 1,
"created_at": "2023-01-10T12:18:47Z",
"creator": "dschief001",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3915,
"state": "closed",
"title": "Rstudio 2022.12.0 Build 353 Quarto Preview option not available",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3915"
}
|
for some reasons the feed does not work in my blog when I use:
https://simplepie.org/demo/?feed=https://jrcuesta.quarto.pub/nir-chemometrics%2Findex.xml
If I click on the link to the blog gives a 404 error, and for other side the images does not appear.
Please let me know if something can be done
Thanks
|
{
"assignee": "dragonstyle",
"comments": 9,
"created_at": "2023-01-10T11:59:57Z",
"creator": "jrcuesta",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 3916,
"state": "closed",
"title": "Problems with the feed in my quarto blog",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3916"
}
|
### Bug description
## Description
The behaviour of `abstract-title` is not consistent with other metadata labels. Other labels like `author-title` and `published-title` can be specified under `format` *or* the top level of a document, but `abstract-title` only works when specified at the top level. As a consequence you can't provide your own abstract title in Quarto extensions.
The expected behaviour is that the abstract title should be "My Abstract" in both examples below.
## Reprex
Here the abstract title remains as "Abstract":
```qmd
---
title: "Reprex"
author: First Last
date: 2023-01-09
abstract: Some abstract text
format:
html:
author-title: My Author
published-title: My Date
abstract-title: My Abstract
---
Some body text
```
Here the abstract changes to "My Abstract":
```qmd
---
title: "Reprex"
author: First Last
date: 2023-01-09
abstract: Some abstract text
format:
html:
author-title: My Author
published-title: My Date
abstract-title: My Abstract
---
Some body text
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] 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": 0,
"created_at": "2023-01-10T00:49:33Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3911,
"state": "closed",
"title": "Inconsistent behaviour providing your own `abstract-title` metadata label",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3911"
}
|
See https://github.com/quarto-dev/quarto-cli/discussions/3899
This works
````markdown
---
title: "Document"
format:
html:
embed-resources: false
---
```{r}
knitr::opts_chunk$set(dev = c("png", "pdf", "svg"))
```
```{r}
library(ggplot2)
ggplot() + ggtitle("this is a title")
```
````
But setting option in YAML does not
````markdown
---
title: "Document"
format:
html:
embed-resources: false
knitr:
opts_chunk:
dev:
- png
- pdf
- svg
---
```{r}
library(ggplot2)
ggplot() + ggtitle("this is a title")
```
````
Error is
````
processing file: test2.qmd
|................................... | 67% (unnamed-chunk-1)Quitting from lines 15-17 (test2.qmd)
Error in `auto_exts[x]`:
! type 'list' d'indice incorrect
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)
8. knitr:::process_group.block(group)
9. knitr:::call_block(x)
10. knitr:::block_exec(params)
11. knitr:::eng_r(options)
12. knitr:::dev2ext(options)
ExΓ©cution arrΓͺtΓ©e
````
Why is that ?
It seems something is missing when letting Quarto set the default knitr options
|
{
"assignee": "cderv",
"comments": 0,
"created_at": "2023-01-09T21:46:51Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3909,
"state": "closed",
"title": "Error setting multipe dev value in knitr opts_chunk in YAML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3909"
}
|
From https://github.com/quarto-dev/quarto-r/issues/40
Simple `.qmd` document with only inline code syntax, starting with `r`
````markdown
`r ** 2`
````
This will be recognized as R inline code and knitr engine will be required. However, for users doing only markdown writing this is surprising.
Unfortunate syntax clash in our discovery.
I don't know if we can do better, but I was thinking maybe only code cells should trigger engine - Will it be that common to only have R inline code in a document without a code cell in the document ?
Anyway, probably worth considering if we can.
|
{
"assignee": "cscheid",
"comments": 6,
"created_at": "2023-01-09T21:34:08Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3908,
"state": "closed",
"title": "Auto binding will use knitr engine when only a inline code syntax is in the doc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3908"
}
|
### Bug description
I am attempting to use quarto with jupyter on my macbook and it is failing to find the python3 kernel despite it being installed (and findable by jupyter).
See the following,
```shell
> quarto check jupyter
[β] Checking Python 3 installation....OK
Version: 3.10.9
Path: /opt/homebrew/opt/[email protected]/bin/python3.10
Jupyter: 5.1.2
Kernels: ir
NOTE: No Jupyter kernel for Python found
```
```shell
> jupyter kernelspec list
Available kernels:
python3 /opt/homebrew/lib/python3.10/site-packages/ipykernel/resources
ir /usr/local/share/jupyter/kernels/ir
```
This is occurring with both 1.2.313 and 1.3.91 and I do not see the same behavior with equivalent versions of quarto (and pip packages) on a linux machine.
System details:
```r
> sessioninfo::session_info()
β Session info ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
setting value
version R version 4.2.2 (2022-10-31)
os macOS Ventura 13.2
system aarch64, darwin21.6.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/New_York
date 2023-01-09
rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
pandoc 2.19.2 @ /opt/homebrew/bin/pandoc
β Packages ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
package * version date (UTC) lib source
cli 3.5.0 2022-12-20 [1] CRAN (R 4.2.2)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
[1] /Users/rundel/Library/R/arm64/4.2/library
[2] /opt/homebrew/Cellar/r/4.2.2/lib/R/library
βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 1,
"created_at": "2023-01-09T17:24:59Z",
"creator": "rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3902,
"state": "closed",
"title": "Unable to find python3 kernel on MacOS 13.2 (M1)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3902"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3876
<div type='discussions-op-text'>
<sup>Originally posted by **bvancil** January 6, 2023</sup>
Greetings! I'm happy to try to put together an alternative minimal reproducible example in another language if someone can suggest a Jupyter kernel that uses less common comments. I'm trying to label a table with a caption in this example with SAS, which uses an asterisk (*) to begin the comment and a semicolon (;) to end it. It also has C-style /* ... */ comments.
````
---
format:
html:
code-fold: true
jupyter: sas
---
As you can see in Table @table-class, there are people.
```{sas}
*| label: table-class;
*| fig-cap: "Class table";
title;
proc print data = sashelp.class(obs = 4);
run;
```
````
results in
```
YAMLException: bad indentation of a mapping entry (src\quarto\prototype\test_table-caption.qmd, 12:11)
11: *| label: table-class;
12: *| fig-cap: "Class table";
~~
13: title;
```
Getting rid of the figure caption produces output, but the label reference isn't resolved, so I'm clearly specifying the parameters wrongly. Any ideas for how to specify parameters in a way that both SAS and Quarto will like?
### Things I've tried
```
*| label: table-class
*| fig-cap: "Class table"
;
```
Result: Quarto doesn't complain, but neither the caption nor the reference work.
```
/*
*| label: table-class
*| fig-cap: "Class table"
*/
```
Result: Same
```
/*
#| label: table-class
#| fig-cap: "Class table"
*/
```
Result: Same
</div>
|
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-01-09T16:28:27Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "v1.3",
"number": 3901,
"state": "closed",
"title": "How to specify cell parameters for languages with unusual comments",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3901"
}
|
To avoid confusion like that in #3880, we should explicitly document the required order in fenced div attributes (this will become more acute as we lean into div and span classes more strongly to denote custom elements.)
|
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-01-09T16:21:30Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"lint"
],
"locked": false,
"milestone": "Future",
"number": 3900,
"state": "open",
"title": "Document fenced div attribute syntax",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3900"
}
|
The discussion comments suggest the `layout` option is the culprit:
````
```{r echo=FALSE, fig.height=30, layout="l-page"}
cross_plot_clean
```
````
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3761
<div type='discussions-op-text'>
<sup>Originally posted by **werkstattcodes** December 26, 2022</sup>
Hello,
I am moving some posts from my distill blog to quarto. In several instances, I get the following error message when rendering the posts with quarto:
```
Error running filter C:/Users/Roland/AppData/Local/Programs/Quarto/share/filters/layout/layout.lua:
...ata\Local\Programs\Quarto\share\pandoc\datadir\_json.lua:167: bad 'for' initial value (number expected, got nil)
stack traceback:
...ata\Local\Programs\Quarto\share\pandoc\datadir\_json.lua:381: in function '_json.decode'
...ta/Local/Programs/Quarto/share/filters/layout/layout.lua:3754: in function 'parseLayoutWidths'
...ta/Local/Programs/Quarto/share/filters/layout/layout.lua:4419: in function 'layoutCells'
...ta/Local/Programs/Quarto/share/filters/layout/layout.lua:4240: in function <...ta/Local/Programs/Quarto/share/filters/layout/layout.lua:4233>
ERROR: unexpected character 'l' at line 1 col 1
```
Any idea what this could be due to? I can run all cells (Quarto: Run All Cells) without the problem. The code of one such post would be available [here](https://github.com/werkstattcodes/distill_clean/blob/master/_post/2020-03-02-primary-schools-in-vienna/primary-schools-in-vienna.Rmd).
Any hint most welcome. Many thanks!
PS: I think I saw somewhere a function which allows rendering a document only up to a specific point (in contrast to the entire document). If anyone knows what I mean, it would help me to isolate the issue to i.e. a specific chunk. Thanks again.
</div>
|
{
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"created_at": "2023-01-09T15:57:23Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3897,
"state": "closed",
"title": "lua error message when rendering blog post",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3897"
}
|
### Bug description
First of all, thank you for the amazing tool!
I'm trying to produce an HTML report from .QMD and getting the following error:
> ERROR: TypeError: Cannot read properties of undefined (reading 'startsWith')
It seems to be related to dyno-dom (as per debug log):
> Error loading deno-dom-native: Could not open library: Could not open library: dlopen(/Applications/quarto/bin/tools/deno_dom/libplugin.dylib, 0x0005): tried: '/Applications/quarto/bin/tools/deno_dom/libplugin.dylib' (mach-o file, but is an incompatible architecture (have (x86_64), need (arm64e)))
Out of curiosity, when / why does deno-dom-native gets triggered? This is the first time I saw error and I've been using Quarto for >6 months. It would help me isolate the problem.
**Steps:**
- I ran: `quarto render _analysis_1/prediction.qmd --to html`
- Jupyter notebook gets produced (and everything looks okay, nothing out of place), assets are saved in a separate folder
- But then the error gets triggered when creating the HTML self-contained file
- The following error shows up:
> ERROR: TypeError: Cannot read properties of undefined (reading 'startsWith')
**Version:**
- I have ARM64 / Mac M1 architecture
- System: Mac OS Monterey (12.5.1 (21G83))
- I tried both 1.2.269 and 1.3.91 (pre-release) -- all checks pass
**Eliminating possible causes:**
- Is it common? No, I have produced several different reports earlier today, there were no significant differences between them
- Are there some large / unusual attachments, formats, etc? No.
**Troubleshooting steps:**
- I ran with `-log-level debug`, see the above error message about dyno-dom-native not being the right version (for ARM64_
- I ran `quarto check` -- all passes
- Updated Quarto to latest release and pre-release + ran quarto check -- all passes
- Tried to manually update dyno-dom to the latest release (0.1.35 supports ARM64) -- no difference
I'm unable to provide the underlying jupyter notebook due to confidentiality issues -- I'll try to reduce it and reproduce the error.
YAML Header
```md
---
title: Some title
author: Some name
date: 2022-01-09
format:
html:
toc: true
toc-depth: 2
code-fold: true
self-contained: true
revealjs:
auto-stretch: true
self-contained: true
scrollable: true
incremental: true
preview-links: auto
slide-number: true
transition: slide
background-transition: fade
fig-align: center
jupyter: julia6-1.8
---
```
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 5,
"created_at": "2023-01-09T15:02:59Z",
"creator": "svilupp",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3896,
"state": "closed",
"title": "Error loading deno-dom-native / Cannot read properties of undefined (reading 'startsWith')",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3896"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3798
<div type='discussions-op-text'>
<sup>Originally posted by **justanothergithubber** December 29, 2022</sup>
Is it possible to move "Other Formats" that is normally located in the margin sidebar at the right to the left? (like Table of Contents which is controlled by `toc-location`) This gives more space for main content when `page-layout` is set to `full`.</div>
|
{
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-09T13:40:57Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3895,
"state": "open",
"title": "Move \"Other Formats\"",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3895"
}
|
## Description:
Embedding local videos with the video shortcode fails.
## Steps to Reproduce:
- Create `index.qmd`
Where `local-video.mp4` is in the same directory as `index.qmd`.
```
---
format:
revealjs:
embed-resources: true
---
{{< video local-video.mp4 >}}
```
or
```
---
format:
html:
embed-resources: true
---
{{< video local-video.mp4 >}}
```
- `quarto preview index.qmd`
### Expected Result:
The video loads and is playable just like it would be if `embed-resources: false`
### Actual Result:
The video doesn't load.
reveal-js: an error message `No compatible source was found for this media.` is displayed.
html: no error message, video is not playable
#### Workaround
- Use `` instead of the shortcode. The video is not responsive.
- `embed-resources: false`
----
### Bug description
Hi,
I would like to build a self contained html-revealjs with local videos. Yet, `embed-ressources: true` does not include videos added with `{{< video local-video.mp4 >}}` while it does with `background-video="local-video.mp4"` (Ubuntu 22.04, quarto v1.2).
```md
---
title: ""
format:
revealjs:
embed-resources: true
---
## {background-video="local-video.mp4"}
##
{{< video local-video.mp4 >}}
```
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 6,
"created_at": "2023-01-09T10:56:41Z",
"creator": "Balaika",
"is_pull_request": false,
"labels": [
"bug",
"video"
],
"locked": false,
"milestone": "v1.4",
"number": 3892,
"state": "open",
"title": "Embedding local videos with the video shortcode fails.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3892"
}
|
### Bug description
Unless I missed something, it seems that the anchor symbols do not appear for headers of level 1.
On your documentation site built with Quarto, it isn't an issue as your top level is `h2` (`## Some section title`), but on my site, I am starting at level 1 and I am missing those nice easy anchors for all `h1` (`# Some section title`) headers.
Here is one of the pages of the site to test it out: https://mint.westdri.ca/git/intro.html.
I did not add anything in my yml file on this nor did I customize anything linked with this.
Thank you!
---
OS: Arch Linux (6.1.3-arch1-1)
### 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": 8,
"created_at": "2023-01-09T03:05:00Z",
"creator": "prosoitos",
"is_pull_request": false,
"labels": [
"bug",
"lint"
],
"locked": false,
"milestone": null,
"number": 3891,
"state": "closed",
"title": "Anchors not showing while hovering over headers of level 1 (h1)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3891"
}
|
### Bug description
On a fresh install on Windows 10, I run into the following error when doing `quarto check` (or when trying to preview):
```
ERROR: NotFound: The system cannot find the file specified. (os error 2), remove 'C:\Users\Jakob\AppData\Local\quarto\sass\397ef2e52d54cf686e4908b90039e9db.css'
```
This seems to be the same error reported [here](https://community.rstudio.com/t/quarto-check-error-notfound-css-file/152507) and occurred both via the 1.2.313 MSI downloaded from the website as well as with an installation via winget, which seems to be a slightly older version.
### 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?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "dragonstyle",
"comments": 22,
"created_at": "2023-01-07T14:23:07Z",
"creator": "jfb-h",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"windows",
"stale"
],
"locked": false,
"milestone": "v1.4",
"number": 3883,
"state": "open",
"title": "Missing .css file after fresh install",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3883"
}
|
### Bug description
This bug requires a bit of setup, so I've included a zip file with a reprex website: [reprex-website.zip](https://github.com/quarto-dev/quarto-cli/files/10365861/reprex-website.zip).
## Terminology
I'm using the term "series" to refer to a listing page that lists listing pages. The latter listing pages list posts which are related to each other by some topic.
This works really great by the way; you can even add a sidebar to get navigation between the posts in the series (almost like a lighter version of the book format inside a website).
## Bug description
I want to add citations to the posts inside a series with a citation style that includes the post URL by setting `citation: true` and the appropriate CSL. However, when I do this, the URLs for the posts are incorrect.
For example, say my `site-url` is `https://reprex.com`. I have a series called `my-awesome-series` and a post in that series is called `a-first-post`. The URL to this post is `https://reprex.com/series/my-awesome-series/posts/first-post.html`. **This should be the URL included in the post citation**. Instead, the URL in the citation thinks the post is located in the root directory of the site: `https://reprex.com/first-post.html`.
Site navigation works fine, so it's just the citation URL that seems to be the issue.
## How to reproduce
Using the reprex site, you can preview the site to see the bug. From the home page, click the "My awesome series" post, then click either of the two posts there and see the URL at the end of the citation at the bottom of the page. If you compare that to the URL in the browser, you can see it's ignoring the nesting structure of the site.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-07T09:30:18Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3881,
"state": "closed",
"title": "Citation URLs are wrong in posts of nested listing pages when `citation: true`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3881"
}
|
### Bug description
Hello everyone
I'm having difficulties with crossreferencing a table in a separate document. Does crossreferencing between documents, which are included with the include-shortcode in a main file, even work?
I have a table in a file called `linux_bash_commands.qmd` that is given the following parameters, including the reference `#tbl-bash-commands`. The table compiles fine.
``` qmd
: Table of Linux Commands {tbl-colwidths="[20,20,25,35]" #tbl-bash-commands}
```
In another file called `linux_and_raspberry_pi4.qmd` I try to reference the table with following snippet.
``` qmd
Siehe @tbl-bash-commands
```
Both files `linux_and_raspberry_pi4.qmd` & `linux_bash_commands.qmd` are included in a main file called `main_aprog.qmd`. Following shows the contents of the file.
``` qmd
---
title: "Some interesting title"
author: "Some Authors"
date: "01.01.2023"
lang: de
# [RENDER CONFIGURATION] ==============================
format:
pdf:
include-in-header:
- config.tex
pdf-engine: pdflatex
# [DOCUMENT CONFIGURATION] ============================
geometry:
- "top=25mm"
- "bottom=30mm"
- "left=15mm"
- "right=15mm"
papersize: a4paper
fontsize: 9pt
code-block-border-left: false
code-block-bg: "#f7f7f7"
toc: true
toc-depth: 3
number-sections: true
number-depth: 3
pagenumbering: none
highlight-style: github
---
...
# Linux & Raspberry Pi 4
{{< include chapters/linux_and_raspberry_pi4.qmd >}}
...
{{< include chapters/linux_bash_commands.qmd >}}
...
```
Compiling the document results in following result:
---
Quarto Version: 1.2.280
OS System: 64-Bit Windows 10 Pro
LaTex Version: pdfTeX 3.14159265-2.6-1.40.21 (TeX Live 2020/W32TeX)
### 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": 4,
"created_at": "2023-01-07T08:01:30Z",
"creator": "joelvonrotz",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3880,
"state": "closed",
"title": "Crossreferencing between documents doesn't work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3880"
}
|
As you probably know, [Hugo renders content](https://gohugo.io/content-management/organization/) from a path such as `content/section/my_page.md` to `publish/section/my_page/index.html`. This breaks the default image links, which assumes the rendered version remains at the same directory depth, instead of being promoted from `section/` to `section/my_page`. Thus `index.html` will contain figure links like `my-page.markdown_strict_files/figure-markdown_strict/pressure-1.png` which do not resolve, because it should be `../my-page.markdown_strict_files/figure-markdown_strict/pressure-1.png`.
I thought I might be able to work around this with knitr `fig.path` options, but that just opens a rabbit hole (e.g. `fig.path="../`" doesn't help any, but has the side effect of two copies of the figure being created, one with `my-page.markdown_strict_files/figure-markdown_strict` path and one with no additional path. The `.md` and `.html` use the one with no additional path, but this only causes more chaos with hugo's mapping conventions....
|
{
"assignee": "cscheid",
"comments": 3,
"created_at": "2023-01-07T00:26:10Z",
"creator": "cboettig",
"is_pull_request": false,
"labels": [
"hugo"
],
"locked": false,
"milestone": "v1.3",
"number": 3930,
"state": "closed",
"title": "figure paths are broken in hugo-md format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3930"
}
|
### Bug description
Adding a label to a chunk will create an empty figure caption when `fig-cap` is undefined (this happens with the knitr-style syntax for chunk labels too). Figure captions should only appear if you opt into them with `fig-cap`, so this feels like a bug.
Here's a reprex:
````qmd
---
title: "Reprex"
format: html
---
```{r}
#| label: fig-cars
plot(cars)
```
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 3,
"created_at": "2023-01-06T23:07:02Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3878,
"state": "closed",
"title": "Chunk labels create empty figure captions when `fig-cap` is undefined",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3878"
}
|
Currently, `fig-alt` does not work for mermaid diagram. However, there seems a workaround. Mermaid has their own [accessibility options](https://mermaid.js.org/config/accessibility.html).
@cscheid -- We may want to bind `fig-cap` to `accTitle` and `fig-alt` to `accDescr`. Other additional accessibility fixes that I am not mentioning here need to be taken care of on mermaid side.
## Reprex
````
---
title: "Untitled"
format: html
---
# Mermaid Accessibility
## Inaccessible Version
```{mermaid}
%%| fig-alt: testing
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
```
## Accessible Version
```{mermaid}
graph LR
accTitle: Big Decisions
accDescr: Bob's Burgers process for making big decisions
A[Identify Big Descision] --> B{Make Big Decision}
B --> D[Be done]
```
````
|
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2023-01-06T17:20:41Z",
"creator": "jooyoungseo",
"is_pull_request": false,
"labels": [
"bug",
"accessibility",
"mermaid"
],
"locked": false,
"milestone": "v1.4",
"number": 3873,
"state": "open",
"title": "[Accessibility] fig-alt does not work for mermaid",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3873"
}
|
The following document renders properly in quarto 1.2, but incorrectly (with cross ref warning as well) in quarto 1.3. The figure appears to not be processed properly when inside the callout.
```
---
title: Xref Test
format: html
---
::::{.callout-note}
Hi there, I'm putting a figure in a call and then referencing it.
:::{#fig-foobar fig-cap="This is a figure in a callout"}
FIGURE
:::
::::
:::{#fig-foobar2 fig-cap="This is a figure2 in a callout"}
FIGURE2
:::
See @fig-foobar, @fig-foobar2.
```
|
{
"assignee": "cscheid",
"comments": 1,
"created_at": "2023-01-06T15:29:41Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3872,
"state": "closed",
"title": "Cross Referencing Inside Callouts Not Working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3872"
}
|
### Bug description
Hi,
I have a multi page quarto website, with a `index.qmd` and multiple linked chapters in a chapters folder.
When I try and render the `index.qmd` it sometimes works and sometimes doesn't with the error:
> ERROR: The directory name is invalid. (os error 267), readdir 'C:\<address>\index_files\desktop.ini' for path "C:\<address>\index_files\desktop.ini"
It was the case that the folder `index_files` persisted from a previous attempt to render the site, and deleting it would let the site render, but that's not working now
- Windows 10 Home
- RStudio 2022.12.0 Build 353
I have google drive running and thought it might be that locking the `index_files` folder to stop it deleting. I've tried to find this issue raised elsewhere, but haven;t had any luck. Annoyingly it;s very hard to reproduce, but does occur on the same project being run on both my laptop and desktop
### 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": "cderv",
"comments": 4,
"created_at": "2023-01-06T15:10:13Z",
"creator": "peterejkemp",
"is_pull_request": false,
"labels": [
"bug",
"windows",
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 3871,
"state": "open",
"title": "Rendering: ERROR: The directory name is invalid",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3871"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3862
<div type='discussions-op-text'>
<sup>Originally posted by **fredguth** January 5, 2023</sup>
I decided to download the 1.3.83 pre-release version and noticed that a template I created (`fredguth/tufte-quarto`) is not working properly in this version.
This leads me to question:
- **What is the version strategy of quarto and when should I think about updating my templates to a new version?**
I couldn't find anything specific about templates in the pre-release documentation (https://quarto.org/docs/prerelease/1.3.html)
</div>
|
{
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-06T13:18:32Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3870,
"state": "closed",
"title": "Pre-release version with custom templates",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3870"
}
|
### Bug description
I want to make use of the HTML [`<template />` tag](https://developer.mozilla.org/en-US/docs/Web/HTML/Element/template) to allow me to create DOM elements which I can then reuse via JavaScript.
I am quarto feature [include-after-body](https://quarto.org/docs/output-formats/html-basics.html#includes) to insert the HTML.
When I try to read or clone the template, I only get `#document-fragment` without the stuff inside my `<template />` declaration. when I view source on the HTML output from Quarto, it seems that the `<template />` tag itself is still present, but in the source code its an empty tag.
For example, if I define a template like
```html
<template id="productrow">
<tr>
<td class="record"></td>
<td></td>
</tr>
</template>
```
When I go to view source on the quarto output html file, I only see:
```
<template id="productrow"></template>
````
The tag has been emptied of is children elements somewhere in the rendering process it seems (?)
I am exporting to a revealjs presentation if that makes a difference, but I couldn't find anything about revealjs and `<template />` issues.
Here is a very small `*.qmd` that shows the same issue:
```
---
format:
revealjs:
hash: true
self-contained: false
---
## Some Slide
<table id="producttable">
<thead>
<tr>
<td>UPC_Code</td>
<td>Product_Name</td>
</tr>
</thead>
<tbody>
<!-- existing data could optionally be included here -->
</tbody>
</table>
<template id="productrow">
<tr>
<td class="record"></td>
<td></td>
</tr>
</template>
```
When you render (I am rendering using the button in the VSCode plugin on Windows) and then vie source you will see:
```
...
</tbody>
</table>
<template id="productrow"></template><p></p>
<div class="footer footer-default">
...
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 4,
"created_at": "2023-01-05T19:39:22Z",
"creator": "erichgoldman",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3864,
"state": "closed",
"title": "Content of HTML <template /> tag is stripped",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3864"
}
|
The documentation for [conditional content](https://quarto.org/docs/authoring/conditional.html) only discusses the use of divs, but you can also use inline CSS for conditional content. It would be nice if this was documented on the conditional content page too.
Here's a reprex .qmd for demonstration:
```qmd
---
title: "Reprex"
format:
pdf: default
html: default
---
::: {.content-visible when-format="html"}
Will only appear in HTML. (div)
:::
::: {.content-visible when-format="pdf"}
Will only appear in PDF. (div)
:::
[Will only appear in HTML. (inline)]{.content-visible when-format="html"}
[Will only appear in PDF. (inline)]{.content-visible when-format="pdf"}
```
|
{
"assignee": null,
"comments": 1,
"created_at": "2023-01-05T19:19:36Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "Future",
"number": 3863,
"state": "open",
"title": "Document inline conditional content",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3863"
}
|
### Bug description
I'm having a problem with the headings of unnumbered sections if they are after a numbered section (or table of contents). Somehow they inherit the headings from the last numbered section (or table of contents).
Here is a reproducible example:
**Second Preface page inherits "Table of contents" heading**
**Second References page inherits "Table of contents" heading**
This is my _quarto.yml file, and I'm using the standard content created with a Quarto book:
```
project:
type: book
output-dir: _book
book:
chapters:
- index.qmd
- references.qmd
- summary.qmd
bibliography: references.bib
format:
pdf:
documentclass: book
toc: true
```
One "solution" is to number the section. However I do not want some sections (e.g., preface, acknowledgments) to be numbered chapters.
Here is some additional information:
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
Rstudio:
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Ubuntu Jammy
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
**Ubuntu 22.04 LTS**
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 1,
"created_at": "2023-01-05T10:17:54Z",
"creator": "SbastianGarzon",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3854,
"state": "closed",
"title": "Heading bug (PDF-unnumbered sections)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3854"
}
|
To reproduce
* Clone `quarto-journals/acs`
* `quarto render template.qmd`
This will error like this
````
$ quarto render template.qmd
ERROR: La syntaxe du nom de fichier, de rΓ©pertoire ou de volume est incorrecte. (os error 123), stat 'C:\Users\chris\Documents\DEV_R\quarto-journals\acs\_extensions\acs\_extensions\quarto-ext\latex-environment\C:\Users\chris\Documents\DEV_R\quarto-journals\acs\_extensions\acs\_extensions\quarto-ext\latex-environment\latex-environment.lua'
Error: La syntaxe du nom de fichier, de rΓ©pertoire ou de volume est incorrecte. (os error 123), stat 'C:\Users\chris\Documents\DEV_R\quarto-journals\acs\_extensions\acs\_extensions\quarto-ext\latex-environment\C:\Users\chris\Documents\DEV_R\quarto-journals\acs\_extensions\acs\_extensions\quarto-ext\latex-environment\latex-environment.lua'
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 getFilter (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/filters.ts:682:8)
at resolveFilterExtension (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/filters.ts:710:21)
at resolveFilters (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/filters.ts:572:19)
at generateDefaults (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/defaults.ts:44:35)
at runPandoc (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/pandoc.ts:261:28)
at renderPandoc (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render.ts:164:30)
at async Object.onRender (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:558:30)
at async renderFiles (file:///C:/Users/chris/Documents/DEV_R/quarto-cli/src/command/render/render-files.ts:506:13)
````
Issue is with Extension directory being prepended to an already absolute path for the filter extensions
https://github.com/quarto-dev/quarto-cli/blob/9aca80aeb66faa07f93a3939453f658ccfd25075/src/extension/extension.ts#L916-L921
In debugging session, we can see that
* `extensions[0].path` is absolute path `"C:\\Users\\chris\\Documents\\DEV_R\\quarto-journals\\acs\\_extensions\\acs\\_extensions\\quarto-ext\\latex-environment"`
* Filter is already an absolute path : `"C:\\Users\\chris\\Documents\\DEV_R\\quarto-journals\\acs\\_extensions\\acs\\_extensions\\quarto-ext\\latex-environment\\latex-environment.lua"`
So the join does create the wrong path in
https://github.com/quarto-dev/quarto-cli/blob/9aca80aeb66faa07f93a3939453f658ccfd25075/src/extension/extension.ts#L938
This does not happens with Shortcodes (`jss` which only have embeded shortcodes works fine).
After a quick discussion with @dragonstyle :
* It seems issue is not Windows specific
* Our tests seems to have miss it - maybe we need to see why
* Nothing really change in extension, but there was some heavy work on Lua filter. Maybe we resolved to absolute earlier than before or differently ? (cc @cscheid)
Easy solution would be to not join paths if the filter path is already absolute path, but I feel this issue could be a regression from somewhere else and maybe this is not the only side effect. So I am looking.
|
{
"assignee": null,
"comments": 0,
"created_at": "2023-01-04T18:57:27Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3850,
"state": "closed",
"title": "Lua Filters in embeded extensions is wrongly resolved ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3850"
}
|
(edit: small change to correct a typo)
### Bug description
When creating a Jupyter notebook using Quarto, I'm attempting to use fenced divs to explicitly separate notebook cells, using the examples in the [Pandoc manual](https://pandoc.org/MANUAL.html#jupyter-notebooks).
This works for a simple example when I do `quarto render simple.qmd --to ipynb` - the second section is rendered in a new cell. (I'm running on Windows 10, Quarto v1.2.280)
````
---
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.
::::::
````
However, when I attempt to make the content conditional as well, all the content is combined in one Markdown cell.
````
---
title: Conditional version
---
::: {.content-visible when-format="ipynb"}
# Lorem ipsum
**Lorem ipsum** dolor sit amet, consectetur adipiscing elit. Nunc luctus
bibendum felis dictum sodales.
:::::: {.cell .markdown}
# Lorem
**Lorem ipsum** dolor sit amet, consectetur adipiscing elit. Nunc luctus
bibendum felis dictum sodales.
::::::
:::
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 1,
"created_at": "2023-01-04T15:23:34Z",
"creator": "tomsutch",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3847,
"state": "closed",
"title": "ipynb output: explicitly separating notebook cells not possible with conditional content",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3847"
}
|
Using a previous version of quarto (1.1.189) I had added some custom rules to a scss file that tweaked the formatting of the title/subtitle/author/institute fields on the title slide (size, bolding, italics, alignment etc) - in particular I had aligned all of the text to the left using the following rule:
```
#title-slide {
text-align: left;
}
```
Which worked fine.
I've just updated my RStudio and quarto has been updated to1.2.269, and the author and institution fields no longer obey the previous formatting rules. After a bit of tinkering I figured out the names of the author and title fields had changed to quarto-title-author-name and quarto-title-affiliation, and changing those in my scss I can get them to change size, bolding etc, but I cannot get them to align left, whether I set the rule as above, or specifically to quarto-title-author-name and quarto-title-affiliation.
Here is a very simple example that recreates the problem at my end, with a scss file called 'test.scss':
qmd file:
```
---
title: "This should be red"
subtitle: "This should be aqua"
author: "This should be green"
institute: "This should be orange"
format:
revealjs:
theme: test.scss
---
```
test.scss contains:
```
/*-- scss:rules --*/
#title-slide {
text-align: left;
}
#title-slide .title {
color: #FF0000;
}
#title-slide .subtitle {
color: #00FFFF;
}
#title-slide .quarto-title-author-name {
color: #00FF00;
}
#title-slide .quarto-title-affiliation {
color: #FFA500;
}
```
Or alternatively,
```
/*-- scss:rules --*/
#title-slide .title {
color: #FF0000;
text-align: left;
}
#title-slide .subtitle {
color: #00FFFF;
text-align: left;
}
#title-slide .quarto-title-author-name {
color: #00FF00;
text-align: left;
}
#title-slide .quarto-title-affiliation {
color: #FFA500;
text-align: left;
}
```
I know I'm tapping into the correct fields because the colour rules are obeyed, but I am stumped as to why the author and affiliation fields are staying centre aligned - not sure if this is a bug or I am just missing something somewhere and just need a different rule (I would guess the latter...).
Help much appreciated!
|
{
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2023-01-04T09:48:43Z",
"creator": "drcaprosser",
"is_pull_request": false,
"labels": [
"verify-fixed"
],
"locked": false,
"milestone": "v1.3",
"number": 3843,
"state": "closed",
"title": "quarto-title-author-name and quarto-title-affiliation not obeying scss text-align on revealjs presentation title slide",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3843"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3836
<div type='discussions-op-text'>
<sup>Originally posted by **agrogan1** January 3, 2023</sup>
Hello! Is there a way to make a quarto book citeable? The Quarto documentation, [Quarto - Creating Citeable Articles](https://quarto.org/docs/authoring/create-citeable-articles.html), would seem to indicate that this is possible for articles but it does not seem to work for books.
In case it's helpful, my book is here, [Multilevel Thinking](https://agrogan1.github.io/multilevel-thinking/), and my YAML is here, [multilevel-thinking/_quarto.yml at main Β· agrogan1/multilevel-thinking Β· GitHub](https://github.com/agrogan1/multilevel-thinking/blob/main/_quarto.yml).
Thank you for any help you can provide.</div>
|
{
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-03T19:34:43Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement",
"books"
],
"locked": false,
"milestone": "v1.4",
"number": 3838,
"state": "open",
"title": "Add `citable article` support for book output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3838"
}
|
We need a fourth argument like `raw_args` that passes arguments untransformed, so that we don't accidentally interpret (eg) URLs with `=` in them as kwargs.
|
{
"assignee": "cscheid",
"comments": 0,
"created_at": "2023-01-03T15:44:48Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3833,
"state": "closed",
"title": "shortcode API needs updating",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3833"
}
|
Just opening a separate issue building on #1323. Icons can now be included in the navbar, but not yet the sidebar.
|
{
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2023-01-03T02:37:04Z",
"creator": "jhelvy",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 3830,
"state": "closed",
"title": "Include icons and text in sidebar ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3830"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3826
<div type='discussions-op-text'>
<sup>Originally posted by **astoeriko** January 2, 2023</sup>
In my document, I would like to have some figures in the main column, and some figures as smaller images in the margin column. The figures in the main column should have their caption in the margin. However, the margin figures should have their captions below the image, not next to them.
I can place the captions of main-column figures in the margin by setting the option `cap-location: margin` in the yaml block.
However, that option messes up my margin figures. They will be too wide for the margin because 1) the image size increases and 2) their captions now appear next to them.
Can I locally override the caption placement? Or can I set it globally but differentiating between main-column and margin figures?
This is a minimum example showing what I mean:
```
---
cap-location: margin
---
{#fig-main-col}
::: {.column-margin}
{#fig-margin-col}
:::
::: {.column-margin}
{#fig-margin-col2}
I can cheat a bit and write my caption below manually. However, it will not be a real caption. For example, it is not numbered, and the vertical spacing seems to be wrong.
:::
```
It looks like this for me:
</div>
|
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"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-03T01:41:56Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3829,
"state": "closed",
"title": "Don't reposition caption in margin figures when `cap-location: margin`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3829"
}
|
### Bug description
We get an spurious reference page when using biblatex citation method in PDF output, because biblatex adds its own header.
### Reproduce
index.qmd
```
# Start
See @knuth84 for discussion of literate programming.
```
_quarto.yml
```
project:
type: book
book:
title: "test"
author: "Jane Doe"
chapters:
- index.qmd
- references.qmd
bibliography: references.bib
format:
pdf:
documentclass: report
cite-method: biblatex
```
Where `references.bib` and `references.qmd` are in the standard quarto project example.
In the PDF output the result is something like:
<img width="186" alt="image" src="https://user-images.githubusercontent.com/98791224/210277202-d766ebcd-6d0b-4cb5-bdef-16a2495640f6.png">
### Possible solution
Generated latex code is:
```
\hypertarget{references}{%
\chapter*{References}\label{references}}
\addcontentsline{toc}{chapter}{References}
\markboth{References}{References}
\printbibliography % this add new header named "Bibliography"
```
To instruct biblatex to not add its own heading, we can replace the last line with:
`\printbibliography[heading=none]`
### More info
- Quarto 1.2.280
- R studio 2022.12.0 Build 353
- Windows 11 Pro 22H2
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 1,
"created_at": "2023-01-02T20:58:01Z",
"creator": "fulem",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3825,
"state": "closed",
"title": "Spurious Reference page when using biblatex in PDF output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3825"
}
|
### Bug description
Proof environment title customization is not working in PDF output when using both `language` and `lang` keywords. It doesn't matter what is the base language or document class.
Reproduce:
index.qmd
```
# Start
::: {#thm-thm}
Foo
:::
::: {.proof}
This block should be titled "Test", but instead is titled "Proof".
:::
```
_quarto.yml
```
project:
type: book
book:
title: "Test"
author: "Jane Doe"
chapters:
- index.qmd
lang: en
language:
en:
environment-proof-title: "Test"
format:
html:
theme: cosmo
pdf:
documentclass: report
editor: visual
```
### Possible solution
The relevant generated latex code is: `\renewcommand*{\proofname}{Test}`
But that is not having any effect. Currently, the title name is obtained from the language line
`\babelprovide[main,import]{english}`.
Instead, generated latex code should be: `\AtBeginDocument{\renewcommand*{\proofname}{Test}}`
More info:
- Quarto 1.2.280
- R studio 2022.12.0 Build 353
- Windows 11 Pro 22H2
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2023-01-02T03:59:47Z",
"creator": "fulem",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3820,
"state": "closed",
"title": "Proof environment title customization not working in PDF output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3820"
}
|
In the [PDF Engines](https://quarto.org/docs/output-formats/pdf-engine.html) page of the Quarto online docs it says that I can install tinytex using the command line:
```
quarto install tinytex
```
However, at least under macOS 13.1 there is no quarto executable anywhere on my hard drive. I did find a Ruby file (quarto.rb) in a homebrew cask, but it's not an executable. Looking at the tinytex docs I was hoping that simply installing it through R (e.g., `install.packages("tinytex")` would solve the problem, but it Quarto apparently doesn't see it. I'm surprised that installing a PDF engine is this hard.
|
{
"assignee": null,
"comments": 6,
"created_at": "2023-01-01T20:04:51Z",
"creator": "rickdonnelly",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3817,
"state": "closed",
"title": "quarto command line installs fails in macOS",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3817"
}
|
I am recycling old R markdown in Quarto. I need to render as pdf to use as class notes. The old code includes references that work.
If I now toggle the RStudio viewer from "Source" to "Visual" and render the pdf, the references fail to appear. If I toggle back I see that [@definetti] has been turned into [\@definetti]. is this a bug? In practice, for my use case, this means I can only work in "Source" or "Visual" but not both, which is not ideal. Alternatives are clunky (e.g. search replace \@ with @ before the final rendering, which is never really final for a living document like class materials).
|
{
"assignee": null,
"comments": 2,
"created_at": "2023-01-01T15:27:09Z",
"creator": "gp1d",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3814,
"state": "closed",
"title": "automatic addition of \\ in front of @ when toggling from \"source\" to \"visual\" and back",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3814"
}
|
Add {.scrollable} to slide title and numbered lists greater than 9 show only the one's digits. In a qmd file add to a slide a list of items 1-15. They can be number with just 1., 1., 1. or 1. 2. 3. But once it gets to 10, the rendered output with reveal.js only show the last single digit.
```
## Slide title {.scrollable}
1.
1.
...
1.
1.
```
(workaround is to use "- 10.")
|
{
"assignee": "cscheid",
"comments": 1,
"created_at": "2023-01-01T07:43:25Z",
"creator": "javajon",
"is_pull_request": false,
"labels": [
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 4283,
"state": "closed",
"title": "Numbered lists greater than 9 show only the one's digits with {.scrollable} slide",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4283"
}
|
The `qmd` file cannot be rendered to `docx` or `pdf` files if it contains mermaid or dot images, although it works for `html` files. If I run
```
quarto preview test.qmd --to docx --no-browser --no-watch-inputs
```
on quarto 1.3.75, it pops up an error message:
```
ERROR: Internal error: temporarily disabled until deno 1.28.* gets puppeteer support
```
If I run it on quarto 1.2.269, it doesn't show or output anything but keeps running the command forever.
I tested this on both Windows 10 and 11.
A minimal reproducible for the `qmd` file can be:
<pre>
---
title: "test"
format: docx
---
## Quarto
```{mermaid}
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
```
</pre>
Everything will work if the mermaid images are removed or the file is rendered to html. Upgrading deno doesn't help.
|
{
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-12-31T03:24:03Z",
"creator": "Jiayou-Chao",
"is_pull_request": false,
"labels": [
"mermaid",
"puppeteer"
],
"locked": false,
"milestone": "v1.3",
"number": 3809,
"state": "closed",
"title": "Quarto cannot render mermaid or dot images to docx and pdf formats",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3809"
}
|
I'm having an issue including just any SVG in LaTeX output---it complains about not having a bounding box, even with height and width defined. I'm using Quarto 1.2.280 and just barely upgraded TinyTex to v2022.12.12. I'm on Ubuntu 18.04 WSL on Windows 11.
`test.svg`:
```svg
<svg xmlns="http://www.w3.org/2000/svg" width="100" height="100">
<circle cx="50" cy="50" r="40" stroke="green" stroke-width="4" fill="yellow" />
</svg>
```
`test.qmd`:
```qmd
# hello there
```
Render, and for me it complains about the bounding box:
```sh
quarto render test.qmd --to pdf
```
```
LaTeX Error: Cannot determine size of graphic in test.svg (no BoundingBox).
See the LaTeX manual or LaTeX Companion for explanation.
```
_Originally posted by @kjohnsen in https://github.com/quarto-dev/quarto-cli/discussions/3283#discussioncomment-4551997_
|
{
"assignee": null,
"comments": 1,
"created_at": "2022-12-30T13:39:47Z",
"creator": "kjohnsen",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3804,
"state": "closed",
"title": "SVGs fail in LaTeX output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3804"
}
|
### Bug description
In the latest version (1.3.75), the following line seems to look for `pagebreak.lua`,
https://github.com/quarto-dev/quarto-cli/blob/912a4962cd361fc092a7f52e720c13199fe39131/src/resources/rmd/execute.R#L187
but the filters seem to have been taken out in this [large commit](https://github.com/quarto-dev/quarto-cli/commit/56888bb94984fd93f16edb42dbe5564c6dc65eaa), with this line
https://github.com/quarto-dev/quarto-cli/blob/912a4962cd361fc092a7f52e720c13199fe39131/package/src/common/prepare-dist.ts#L153
The minimal reproduction example is simple: an empty file with only an `r` code block, or any inline `r` will do as well.
````qmd
```{r}
```
````
where upon trying to render I get errors:
```
Error running filter .../quarto-prerelease/current/share/filters/rmarkdown/pagebreak.lua:
cannot open .../quarto-prerelease/current/share/filters/rmarkdown/pagebreak.lua: No such file or directory
```
As above my `quarto` is 1.3.75 and I am on Windows.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-12-30T03:42:33Z",
"creator": "justanothergithubber",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3801,
"state": "closed",
"title": "Version 1.3.75 breaks R",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3801"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3775
Currently `page-navigation` can only navigate between pages in a sidebar, but not between pages in a blog or listing. It would be a great improvement if it was possible to use `page-navigation` in these cases too.
This is generally nice for blogs, as it might encourage readers to check other posts. But it also opens up the possibility to write a series of related posts under their own listing which users can navigate between, like in [Hugo Apero](https://hugo-apero.netlify.app/blog/spoonful-series/).
|
{
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-12-29T20:29:41Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3795,
"state": "open",
"title": "Support `page-navigation` for blog listings",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3795"
}
|
I have this in my yaml (website):
```
title: "Something Great"
slug: 'something-great'
```
The webpage is at https://somewhere.com/something-great/
so the html is created from a index.qmd file as expected using "quarto render".
When I go add other filetypes such as pdf, revealjs, and tex, I use the following:
```
format:
pdf:
output-file: something-great.pdf
latex:
output-file: something-great.tex
revealjs:
output-file: something-great.html
```
Everything gets generated as expected. All 4 files. index.html, pdf, tex, and html (revealjs).
However, how can I do the same thing without having to do: "something-great" 4 times in the yaml and not have badly named files such as "pdf_document". In other words how can I use the value of the slug key as a value in the output-file key?
Is this the only way to do this?
Thank You.
|
{
"assignee": null,
"comments": 3,
"created_at": "2022-12-29T20:12:46Z",
"creator": "directknowledge",
"is_pull_request": false,
"labels": [],
"locked": true,
"milestone": null,
"number": 3802,
"state": "closed",
"title": "Repeated yaml values",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3802"
}
|
### Bug description
My render fails (at the XeLaTeX part?) whenever I use a custom font. I'm on Ubuntu 18.04 WSL on Windows 11.
`test.qmd`:
```qmd
---
format:
pdf:
mainfont: Arial
---
# Hello there!
This is a test.
```
So, `quarto render test.qmd --to pdf` fails, unless I stop trying to specify the font.
```
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
Fontconfig warning: FcPattern object weight does not accept value [50 200)
updating tlmgr
updating existing packages
compilation failed- error
see test.log for more information.
```
By the way, I always see that Fontconfig weight warning, whether I try to set the font or not. And I'm not a LaTeX expert, but I don't see anything useful [in the log](https://github.com/quarto-dev/quarto-cli/files/10321886/test.log).
Quarto check:
```
[β] Checking Quarto installation......OK
Version: 1.2.280
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.8 (Conda)
Path: /home/kyle/anaconda3/bin/python
Jupyter: 4.7.1
Kernels: conda-env-test2-py, ..., julia-1.8
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
I also just upgraded TinyTex to 2022.12.12.
### 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": 7,
"created_at": "2022-12-29T20:11:45Z",
"creator": "kjohnsen",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 3794,
"state": "open",
"title": "LaTeX crash when using custom font",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3794"
}
|
.
|
{
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-12-29T19:11:42Z",
"creator": "directknowledge",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3796,
"state": "closed",
"title": "citation: true",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3796"
}
|
.
|
{
"assignee": "dragonstyle",
"comments": 14,
"created_at": "2022-12-29T19:07:10Z",
"creator": "directknowledge",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3797,
"state": "closed",
"title": "Citeproc Warning bibliography: value",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3797"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3784
<div type='discussions-op-text'>
<sup>Originally posted by **edalfon** December 29, 2022</sup>
Hi,
We use [includes](https://quarto.org/docs/authoring/includes.html) to re-use content across documents in a Quarto website project.
In this project, we set the [option `execute-dir: project`](https://quarto.org/docs/reference/projects/websites.html) to keep the working directory for computations pinned to the root directory of the project. That way, for example, all documents can refer to `./data/fancy_data`, regardless of which subfolder they are placed in. For us this is important because we organize the content of the project in a bunch of subfolders that can go nested to different depth. Without the `execute-dir: project` the project would simply be much harder to mantain and keep track of the paths we should use in each document.
We expected `{{< include >}}` to follow the same project's `execute-dir` option, but it doesn't seem so. Instead, it always resolves to the same folder of the file you are including content in. So if you are in a subfolder and whant to include some content in the root of the project, you cannot do this `{{< include _codebit.qmd>}}`, but you have to do something like this `{{< include ../../../_codebit.qmd>}}`. And the `../../...` part would depend on where the document lives and if you decide to reorganize the structure of the documents, you would need to update that as well. So, it is a bit of a mess.
We couldn't find a way around this or any other option similar to `execute-dir`, but for the whole working directory of the project and not only for computations.
Wouldn't it be better to have the includes directive to follow the `execute-dir` option?, is there currently any way to do it?</div>
|
{
"assignee": "cwickham",
"comments": 0,
"created_at": "2022-12-29T13:48:39Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"documentation",
"triaged-to",
"includes"
],
"locked": false,
"milestone": "v1.4",
"number": 3788,
"state": "open",
"title": "Better document where project paths (starting with `/` to get to project root) can be used",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3788"
}
|
### Bug description
When using a (home-made) docker image [described here](https://forgemia.inra.fr/jbleger/docker-image-quarto-jax-torch-sphinx/-/blob/4813d874bd42dc6d6d5e33bb28905c443f545ed5/Dockerfile) with quarto and all stuff I need for my computations, I obtain the following error:
```
$ quarto add --no-prompt https://gitlab.com/jbleger/code-block-all/-/archive/main/shorty-main.zip
Downloading
[β] Downloading
[β] Unzipping
ERROR: Error executing 'unzip': No such file or directory (os error 2)
```
I deduce that quarto use the `unzip` tool, which is packaged in debian in `unzip` package which is not included by default on debian.
I should be a good idea to add `unzip` as dependency in the debian package.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-12-29T09:42:18Z",
"creator": "jb-leger",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3785,
"state": "open",
"title": "Debian package doesn't declare unzip as dependency",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3785"
}
|
### Bug description
Probably related to #3178, an issue I am also experiencing. But subsections are being ignored in the ToC, even without child documents.
This:
```
---
title: "test"
format: html
editor: visual
toc: true
toc-location: left
toc-depth: 2
---
# heading 1
## david
## mycroft
# heading 2
## david
## mycroft
```
Produces this:
I am on Windows 11 running RStudio 2022.07.2 Build 576.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 3,
"created_at": "2022-12-28T18:05:18Z",
"creator": "daranzolin",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3778,
"state": "closed",
"title": "ToC does not include all subsections",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3778"
}
|
### Bug description
There is excessive vertical space before definition/theorem/etc environments in latex output.
Reproduce:
```
# Chapter
## Section
### Subsection
#### Subsubsection
Some text before the definition.
::: {#def-def}
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Ut purus elit,
vestibulum ut, placerat ac, adipiscing vitae, felis. Curabitur dictum gravida
mauris.
:::
::: {#exm-exm}
Nam dui ligula, fringilla a, euismod sodales, sollicitudin vel, wisi. Morbi
auctor lorem non justo. Nam lacus libero, pretium at, lobortis vitae, ultricies et, tellus.
:::
Some text before the theorem.
::: {#thm-thm}
Nulla malesuada porttitor diam. Donec felis erat, congue non, volutpat
at, tincidunt tristique, libero. Vivamus viverra fermentum felis.
:::
::: {.proof}
Quisque ullamcorper placerat ipsum. Cras nibh. Morbi vel justo vitae lacus
tincidunt ultrices. Lorem ipsum dolor sit amet, consectetuer adipiscing elit.
In hac habitasse platea dictumst.
:::
Some text afterwards.
```
Quarto configuration is the standard when creating a new quarto project in RStudio. So, the latex class is set as `documentclass: scrreprt`. However, the issue is noticeable in other classes.
Pdf render where the amount of inter space can be appreciated:
<img width="341" alt="image" src="https://user-images.githubusercontent.com/98791224/209750130-ef67d3fa-666b-4d30-8a5f-f9fd7f05bf39.png">
Compare with the hand written latex version using same class:
<img width="331" alt="image" src="https://user-images.githubusercontent.com/98791224/209750343-c58ce541-73ce-4188-866e-5292508e18aa.png">
Examining the generated tex file i see every definition (and similar) environment is prepended with some extra code. For example, for the definition we have:
```
Some text before the definition.
\leavevmode\vadjust pre{\hypertarget{def-def}{}}%
\begin{definition}[]\label{def-def}
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Ut purus elit,
vestibulum ut, placerat ac, adipiscing vitae, felis. Curabitur dictum
gravida mauris.
\end{definition}
```
I don't know what is the purpose of `\leavevmode\vadjust pre{\hypertarget{def-def}{}}` but it is adding unwanted vertical space. In fact, removing it solves the issue.
But there is another thing not related to aforementioned extra code. Note the height where the proof QED symbol (the white box) is placed. In the quarto version is below normal position. From my tests, i see that an empty line between the end of the proof text and the end proof tag makes a difference. That is, quarto generates the proof as follows:
```
\begin{proof}
Quisque ullamcorper placerat ipsum. Cras nibh. Morbi vel justo vitae
lacus tincidunt ultrices. Lorem ipsum dolor sit amet, consectetuer
adipiscing elit. In hac habitasse platea dictumst.
\end{proof}
```
But if we just remove the final empty line to have:
```
\begin{proof}
Quisque ullamcorper placerat ipsum. Cras nibh. Morbi vel justo vitae
lacus tincidunt ultrices. Lorem ipsum dolor sit amet, consectetuer
adipiscing elit. In hac habitasse platea dictumst.
\end{proof}
```
then the QED symbol goes up where we expect it to be.
More info:
- Quarto 1.2.280
- R studio 2022.12.0 Build 353
- Windows 11 Pro 22H2
### 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": 12,
"created_at": "2022-12-28T03:23:56Z",
"creator": "fulem",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3776,
"state": "closed",
"title": "Excessive vertical space before definition/theorem/etc environments in latex output. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3776"
}
|
.
|
{
"assignee": null,
"comments": 0,
"created_at": "2022-12-27T23:22:21Z",
"creator": "directknowledge",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3789,
"state": "closed",
"title": "PDF Links",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3789"
}
|
Hello,
I've been having a really hard time getting Github Actions to render my site. I keep getting this error and wonder if anyone knows how to solve it. I think there is a version issue going on but I don't understand how to fix it
edit:
The build seems to fail, but sometime after the site will still publish. Is this to be expected? In the image below, the summary.qmd build failed but then that git push seemed to still trigger and successfully publish the quarto site. So maybe this is a non issue?
|
{
"assignee": null,
"comments": 7,
"created_at": "2022-12-27T22:16:03Z",
"creator": "DOH-FAA3303",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 4005,
"state": "closed",
"title": "`Cannot read properties of undefined (reading 'map')` on quarto install tinytex",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4005"
}
|
### Bug description
Broken layout when a list is the first child of `.proof`/`.solution`/`.remark` environment.
Reproduce:
```
::: {.proof}
1. First part
2. Second part
:::
::: {.remark}
1. First part
2. Second part
:::
::: {.solution}
1. First part
2. Second part
:::
```
Html render is completely broken:
<img width="146" alt="image" src="https://user-images.githubusercontent.com/98791224/209713201-c6b6900f-003c-438e-9fc3-633c7422ba3f.png">
Pdf render is not that bad, but there is some issue with the position of the list:
<img width="293" alt="image" src="https://user-images.githubusercontent.com/98791224/209713405-2923845d-8442-410b-ae2c-b883fa9c37d8.png">
More info:
- Quarto 1.2.280
- R studio 2022.12.0 Build 353
- Windows 11 Pro 22H2
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-12-27T19:29:05Z",
"creator": "fulem",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3772,
"state": "closed",
"title": "Broken layout when a list is the first child of .proof/.solution/.remark environment.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3772"
}
|
### Bug description
I try to generate a LaTeX table in Julia using PrettyTables.jl
This creates the LaTeX code for the `\begin{tabular} ... \end{tabular}` sections.
1. If I use `#| output: true` that gets inserted in a `verbatim` environment, which prints the LaTeX code in the final document, which is not what I want. It does include the `table` environment and adds a caption and label as expected, though. I can use the `@tbl-label` method to cross-reference in this case.
2. If I use `#| output: asis` the output is inserted as is (as expected). This renders a nice table, however, then I don't get the `table` environment and no caption and label.
3. I use 2, and add the `\begin{table}`, `\caption`, `\label` before the block and the `\end{table}` after. Then I get the correct table, incl. caption, but I cannot use the `@tbl-label` to crossreference, which is annoying, since I want to use HTML export as well. For LaTeX `\ref{tbl-label}` works, but then I'd need to add the "Table" in front of that and it would need more trickery to switch to HTML export.
Is there a way to either make (1) not use the verbatim environment, or (2) honour the float options `#| label` and `#| tbl-cap:`?
### 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?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-12-27T17:39:39Z",
"creator": "TS-CUBED",
"is_pull_request": false,
"labels": [
"bug",
"crossref",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 3770,
"state": "open",
"title": "Code cells with `#| output: asis` ignore `#| tbl-cap` and `#| label:` ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3770"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3763
<div type='discussions-op-text'>
<sup>Originally posted by **ijlyttle** December 26, 2022</sup>
I am working on a PR for pins (rstudio/pins-r#692), and have gotten myself confused about how to use `resources:` in `_quarto.yml`. I don't know if I have found a bug, or if I am just doing it wrong. Hopefully someone can point me in the right direction.
I see this is discussed also in https://github.com/quarto-dev/quarto-cli/discussions/3443.
Here's my `_quarto.yml` file:
```yml
project:
type: website
resources:
- data/board_one
resources:
- data/board_two
```
`board_one` and `board_two` are directories; my goal is that they be copied recursively into `_site/`.
I find this works for `board_two`, even though this `resources:` isn't in the [documented location](https://quarto.org/docs/websites/website-tools.html#site-resources).
However, for `board_one`, it copies the file in the folder, but not the folder inside. I get these warnings when I render locally:
```
WARNING: File 'data/board_one/mtcars/20221226T175420Z-c2702' was not found.
WARNING: File 'data/board_one/mtcars/20221226T175420Z-c2702/data.txt' was not found.
WARNING: File 'data/board_one/mtcars/20221226T175420Z-c2702/mtcars.json' was not found.
```
I have a (hopefully) reproducible [repo](https://github.com/ijlyttle/quarto-pins), rendered and published with an action; here's the [`data` directory](https://github.com/ijlyttle/quarto-pins/tree/gh-pages/data).
I am using quarto 1.3.56.
Thanks!</div>
|
{
"assignee": "cscheid",
"comments": 7,
"created_at": "2022-12-27T14:23:33Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3766,
"state": "open",
"title": "using `resources:` field in `_quarto.yml`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3766"
}
|
.
|
{
"assignee": null,
"comments": 3,
"created_at": "2022-12-26T18:44:16Z",
"creator": "directknowledge",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3803,
"state": "closed",
"title": "Change the title",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3803"
}
|
### Bug description
The cross reference system is broken inside math mode when we want to do theorem proving by equation chaining.
Reproduce:
```
# Test math and theorem proving
::: {#def-mydef}
This definition says that $A = B$.
:::
$$
B = C
$$ {#eq-myeq}
$$
\begin{align}
A \ &= B &&, \text{ by } @def-mydef \\
&= C &&, \text{ by } @eq-myeq \\
\end{align}
$$
Outside math, references to @def-mydef and @eq-myeq work as expected.
```
More info:
- Quarto 1.2.280
- R studio 2022.12.0 Build 353
- Windows 11 Pro 22H2
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-12-26T18:31:33Z",
"creator": "fulem",
"is_pull_request": false,
"labels": [
"duplicate",
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3764,
"state": "closed",
"title": "Cross references broken inside math",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3764"
}
|
repro:
```
# format-variants.qmd
---
format:
pdf+simple:
output-file: simple.pdf
pdf+fancy:
output-file: fancy.pdf
pdf-engine: lualatex
---
This is a test.
```
This will fail with:
```
ERROR: NotFound: No such file or directory (os error 2), open 'format-variants.tex'
NotFound: No such file or directory (os error 2), open 'format-variants.tex'
at async Object.open (deno:runtime/js/40_files.js:55:17)
at async processLines (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/format/pdf/format-pdf.ts:366:16)
at async file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/format/pdf/format-pdf.ts:335:5
at async Object.complete (file:///Users/cscheid/repos/github/quarto-dev/quarto-cli/src/command/render/render.ts:222:11)
```
|
{
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-12-26T14:01:24Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3762,
"state": "closed",
"title": "multiple pdf targets clean up wrongly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3762"
}
|
Hi,
I seeking help to change the color for the text output form the R code execution. The result I want is the text output to be white color, not the black color
I put the following setting for in the scss, but it not working
// Body
$body-color: $gray-400 !default;
$body-bg: $gray-900 !default;
Thanks very much
|
{
"assignee": null,
"comments": 5,
"created_at": "2022-12-25T04:23:17Z",
"creator": "guoruizhong",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 3893,
"state": "closed",
"title": "Can not change the text color for the output of R code",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3893"
}
|
### Bug description
When using a computational `{{< include /project/_toolbox.qmd >}}` at the very bottom of each of my projects e.g. [example](https://github.com/cgoo4/quantumjitter/blob/main/project/footnote/index.qmd), all the site search results then used the title of the `_toolbox.qmd` rather than the title in the project's `.qmd` which weakened the usefulness of the search.
The easy fix was to _not_ have a YAML `title:` in the included document, and the search now uses the title of the respective project.
I'm just raising this in case it's an unintended behaviour or worth noting in the [documentation](https://quarto.org/docs/authoring/includes.html#computations).
### 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?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 1,
"created_at": "2022-12-24T16:55:11Z",
"creator": "cgoo4",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3751,
"state": "closed",
"title": "`title:` in {{< include _foobar.qmd >}} affects site search results",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3751"
}
|
Hi,
I'm trying to embed a video stored on OneDrive / MS Streams. The video shortcode works fine in a browser on its own:
[https://emckclac-my.sharepoint.com/personal/k1926273_kcl_ac_uk/_layouts/15/embed.aspx?UniqueId=4cff1c09-4be9-45ac-a5ee-50649db2c53a](https://emckclac-my.sharepoint.com/personal/k1926273_kcl_ac_uk/_layouts/15/embed.aspx?UniqueId=4cff1c09-4be9-45ac-a5ee-50649db2c53a)
But when I add it to a quarto file like this:
`{{< video https://emckclac-my.sharepoint.com/personal/k1926273_kcl_ac_uk/_layouts/15/embed.aspx?UniqueId=4cff1c09-4be9-45ac-a5ee-50649db2c53a >}}`
It gives the error:
`No video source specified for video shortcode`
The [documentation ](https://quarto.org/docs/authoring/videos.html)for `video` suggests that MS OneDrive/Streams aren't supported, is this due to change?
|
{
"assignee": null,
"comments": 0,
"created_at": "2022-12-23T20:04:07Z",
"creator": "plukethep",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3747,
"state": "open",
"title": "Embedding OneDrive / MS Stream videos not working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3747"
}
|
### Bug description
I observe situations where code listings are not visible in the PDF output document.
The `index.qmd` file listing below renders to [index.pdf](https://github.com/quarto-dev/quarto-cli/files/10292396/index.pdf).
The Python code listing is not rendered / included in the PDF.
The behavior seems to be dependent on other elements/text in the `index.qmd` file .. e.g. if I delete all text or use a smaller mermaid diagram the Python code listing is rendered correctly.
Versions:
- OS:
- Debian GNU/Linux 11 (bullseye)
- Linux 5.10.0-18-amd64
- quarto: 1.2.280
- chromium: 869685
- tinytex: v2022.12.12
- IDE
- VS Code: 1.71.2
- Quarto Plugin 1.59.0
This is my index.qmd file:
````md
---
lang: en
format:
pdf:
documentclass: scrreprt
keep-tex: true
number-sections: true
pdf-engine: pdflatex
---
# Chapter 1
```{mermaid}
%%| echo: false
%%| label: fig-some-figure
%%| fig-cap: some caption
%%| fig-width: QUARTO_FIG_WIDTH
%%| fig-pos: 'H'
classDiagram
class `pkg.Module`
class Realization1 {
__init__(Base)
__call__(x, **kwargs)
}
class Realization2 {
__init__(Base)
__call__(x, **kwargs)
}
class Base {
__call__(x1, x2)* ndarray
__add__(k1, k2) Base
__mul__(k1, k2) Base
}
class Child1 {
__call__(x1, x2) ndarray
}
class Child2 {
__call__(x1, x2) ndarray
}
class Child3 {
__call__(x1, x2) ndarray
}
`pkg.Module` <|-- Realization1
`pkg.Module` <|-- Realization2
`pkg.Module` <|-- Base
Base <-- Realization1
Base <-- Realization2
Base <|-- Child1
Base <|-- Child2
Base <|-- Child3
```
Lorem ipsum dolor sit amet. Et quas doloremque et quae molestias eos assumenda laudantium nam eaque numquam quo ratione iure qui repudiandae consequatur sit consequatur obcaecati. Est maiores ipsum et perferendis molestiae est debitis soluta eum maxime voluptatum ad dicta voluptate 33 inventore nostrum sit dignissimos omnis. Sit error harum et natus reprehenderit qui alias suscipit in perferendis soluta. Aut aliquam molestias qui dolor facilis qui earum ipsa ea voluptas vitae ab placeat assumenda non soluta harum et harum quia?
Et dolor numquam quo iusto repellat et animi natus est internos modi. Et voluptas possimus ad dolorum omnis qui nulla libero et similique voluptas. Rem internos dolorem et quos quas eum dolorem nisi aut odit quae et provident ipsam.
Ea excepturi quia aut nostrum voluptatum At reiciendis dolores qui quam quia. Aut alias quos est similique repellendus aut illum corrupti ut voluptatibus quis.
```{#lst-some-lst .python lst-cap="some listing"}
import numpy as np
x = np.arange(5)
print(x)
```
Lorem ipsum dolor sit amet. Et quas doloremque et quae molestias eos assumenda laudantium nam eaque numquam quo ratione iure qui repudiandae consequatur sit consequatur obcaecati. Est maiores ipsum et perferendis molestiae est debitis soluta eum maxime voluptatum ad dicta voluptate 33 inventore nostrum sit dignissimos omnis. Sit error harum et natus reprehenderit qui alias suscipit in perferendis soluta. Aut aliquam molestias qui dolor facilis qui earum ipsa ea voluptas vitae ab placeat assumenda non soluta harum et harum quia?
Et dolor numquam quo iusto repellat et animi natus est internos modi. Et voluptas possimus ad dolorum omnis qui nulla libero et similique voluptas. Rem internos dolorem et quos quas eum dolorem nisi aut odit quae et provident ipsam.
Ea excepturi quia aut nostrum voluptatum At reiciendis dolores qui quam quia. Aut alias quos est similique repellendus aut illum corrupti ut voluptatibus quis.
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-12-23T06:17:35Z",
"creator": "mamarder",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3742,
"state": "closed",
"title": "Code listings not visible in PDF output format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3742"
}
|
### Bug description
Quarto uses the terms whitelist and blacklist.
https://github.com/quarto-dev/quarto-cli/blob/85c9e303ece91e77a404e04eeeb2bb4270aecfc7/src/resources/editor/devserver/devserver-core.html#L205
https://github.com/quarto-dev/quarto-cli/blob/5bfd77217530c7a79123e90e3ee840e5300d4d4f/src/vendor/cdn.skypack.dev/-/ansi_up%40v5.1.0-ifIRWFhqTFJbTEKi2tZH/dist%3Des2019%2Cmode%3Dimports/optimized/ansi_up.js#L55
https://github.com/quarto-dev/quarto-cli/blob/d16d9f13110e084ef3c5a4b0f9561a5eb5f3158f/src/resources/formats/html/bootstrap/dist/scss/vendor/_rfs.scss#L1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 2,
"created_at": "2022-12-23T04:28:55Z",
"creator": "datakid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3741,
"state": "closed",
"title": "Quarto code and options use terms `blacklist` and `whitelist`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3741"
}
|
### Bug description
1. Create a new book project
`quarto create-project mybook --type book`
2. Update _quarto.yml to add csl file
`csl: ieee.csl`
3. try to render html and see the error
`quarto render --to html`
4. Error:
```
File C:_o-bug.csl not found in resource path
ERROR: File C:_o-bug.csl not found in resource path
```
This is the same error as #2945
_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.
[mybook.zip](https://github.com/quarto-dev/quarto-cli/files/10290963/mybook.zip)
- [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?
```
mybook $ quarto --version
1.2.280
```
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
```
mybook $ systeminfo | findstr /B /C:"OS Name" /C:"OS Version"
OS Name: Microsoft Windows 10 Pr
o
OS Version: 10.0.19042 N/A Build 19042
```
|
{
"assignee": null,
"comments": 3,
"created_at": "2022-12-22T23:38:52Z",
"creator": "ati-ozgur",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3740,
"state": "closed",
"title": "html render does not with custom csl file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3740"
}
|
### Bug description
I recently finished upgrading a server to Posit Workbench 2022.07.2 Build 576.pro12, which bundled Quarto 1.1.189. In case it's relevant, immediately prior, I upgraded the OS in place from Ubuntu 16.04 -> 20.04. When I attempt to test out the Quarto rendering functionality, I get an error.
Steps in IDE are File -> New File -> Quarto Document -> Create (HTML, knitr engine), save as "test2.qmd". _(file attached as [test2.qmd.txt](https://github.com/quarto-dev/quarto-cli/files/10290707/test2.qmd.txt) since GitHub didn't allow the .qmd extension)_
When I test running quarto from a simple SSH terminal, I get similar results. I also tested using a standalone install of version 1.2.280 and got the same results.
Full stack trace of the error is as follows:
```
ERROR: Is a directory (os error 21)
Error: Is a directory (os error 21)
at Object.opSync (deno:core/01_core.js:172:12)
at Object.readTextFileSync (deno:runtime/js/40_read_file.js:41:17)
at readTheme (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:43539:21)
at readHighlightingTheme (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:43502:26)
at resolveTextHighlightingLayer (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:60313:33)
at resolveThemeLayer (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:60378:31)
at resolveBootstrapScss (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:60262:55)
at boostrapExtras (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:63753:25)
at themeFormatExtras (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:64966:16)
at Object.formatExtras (file:///usr/lib/rstudio-server/bin/quarto/bin/quarto.js:64584:96)
```
Output of Quarto Check:
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 12,
"created_at": "2022-12-22T22:17:01Z",
"creator": "msummersgill",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3739,
"state": "closed",
"title": "QMD Rendering Fails - Error: Is a directory (os error 21)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3739"
}
|
when the video id contains two dashes next to each other: i.e. BbTyu8zE--w
This does not work:
{{< video https://www.youtube.com/embed/BbTyu8zE--w >}}
But this does:
{{< video https://www.youtube.com/embed/BbTyu8zE\-\-w >}}
Just FYI
|
{
"assignee": "dragonstyle",
"comments": 8,
"created_at": "2022-12-22T15:27:00Z",
"creator": "directknowledge",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3744,
"state": "closed",
"title": "When using the video shortcut with a YouTube video url",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3744"
}
|
### Bug description
With the following setup,
`index.qmd`:
```
Example Website
```
`create.sh`:
```
#!/bin/sh
mkdir -p example
echo "hello" > example/hello.qmd
```
`_quarto.yml`:
```
project:
type: website
pre-render: sh create.sh
website:
title: Example Website
sidebar:
title: "Example Sidebar"
contents:
- index.qmd
- auto: "example"
```
I see the following error when running `QUARTO_PRINT_STACK=true quarto render`,
```
ERROR: TypeError: Cannot convert undefined or null to object
TypeError: Cannot convert undefined or null to object
at Function.keys (<anonymous>)
at findIndexFile (file:///Applications/quarto/bin/quarto.js:91210:19)
at nodesToEntries (file:///Applications/quarto/bin/quarto.js:91187:36)
at sidebarItemsFromAuto (file:///Applications/quarto/bin/quarto.js:91115:31)
at expandAutoSidebarItems (file:///Applications/quarto/bin/quarto.js:91037:37)
at resolveSidebarItems (file:///Applications/quarto/bin/quarto.js:91660:32)
at sidebarEjsData (file:///Applications/quarto/bin/quarto.js:91651:11)
at sidebarsEjsData (file:///Applications/quarto/bin/quarto.js:91635:32)
at initWebsiteNavigation (file:///Applications/quarto/bin/quarto.js:91273:37)
at Object.preRender (file:///Applications/quarto/bin/quarto.js:95841:15)
```
Re-running the command then works OK, presumably because the `example` directory and `hello.qmd` file now exist before running `quarto render`. I would expect that Quarto would be able to find and render new files created by the `pre-render` script.
I note that when not using `auto` with a subdirectory there is no error thrown, however the new file is simply missing from the sidebar.
## Extra Info
* macOS Ventura (13.0.1, arm64)
* quarto-cli v1.2.280 & v1.3.56
### 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": "dragonstyle",
"comments": 3,
"created_at": "2022-12-22T11:19:41Z",
"creator": "georgestagg",
"is_pull_request": false,
"labels": [
"bug",
"project-scripts"
],
"locked": false,
"milestone": "v1.4",
"number": 3737,
"state": "open",
"title": "Website sidebar auto generation fails for new files created by pre-render script",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3737"
}
|
### Bug description
Hi. I'm trying to render some `.qmd` files to the PDF format with Mermaid/Graphviz diagrams inside. It seems that when the diagrams are labeled, `figure` environments in the generated `.tex` file are nested, which is a little weird for me.
Here's a minimal example.
````md
---
title: "Test"
format:
latex:
default
---
```{dot}
//| label: fig-1
//| fig-cap: a Graphviz figure
digraph G{
A -> B -> C -> D
}
```
````
and the diagram part of the `.tex` output is:
````latex
\begin{figure}
{\centering
\begin{figure}[H]
{\centering \includegraphics[width=5.5in,height=3.5in]{index_files/figure-latex/dot-figure-1.png}}
\end{figure}
}
\caption{\label{fig-1}a Graphviz figure}
\end{figure}
````
So these `figure` environments get nested, despite the desired output:
````latex
\begin{figure}[H]
{\centering \includegraphics[width=5.5in,height=3.5in]{index_files/figure-latex/dot-figure-1.png}}
\caption{\label{fig-1}a Graphviz figure}
\end{figure}
````
Though the problem seems to be harmless to the PDF output with default options, it may cause some unexpected glitches when custom templates are used.
probably related: #821 triggers the same problem.
- quarto version: 1.2.269
- OS: Windows
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-12-22T10:51:26Z",
"creator": "sun123zxy",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3736,
"state": "open",
"title": "labeled Mermaid & Graphviz diagrams generate nested `figure` environments in LaTeX",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3736"
}
|
### Bug description
````
---
title: "Minimal Working Example"
execute:
tidy: true
---
```{r}
#| eval: false
df_ches = read_csv("1999-2014_CHES.csv") %>%
select(country, party, year, galtan) %>%
mutate(
galtan = recode(galtan, "center" = "5", "extreme tan"="10") %>% as.numeric()
)
```
````
When I add it locally in the chunk with #| tidy: true, it works [as.numeric() on a new line], but not globally in the yaml header ][stays on the same line].
R Studio: 2022.12.0 Build 353 on Windows 11
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 2,
"created_at": "2022-12-22T10:21:11Z",
"creator": "benjaminschlegel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3735,
"state": "closed",
"title": "tidy: true globally",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3735"
}
|
### Bug description
quarto 1.3.26, Windows, RStudio Desktop. Make sure you reset everything to see the warning, when run multiple times it does not show.
index.qmd (nothing else)
````
```{r}
library(flextable)
head(mtcars)[,1:6] |>
flextable()
```
````
Background job output on build:
```
Rendering:
[1/1] index.qmd
[WARNING] Could not fetch resource site_libs/tabwid-1.1.2/tabwid.css
Watching files for changes
Browse at http://localhost:6698/
GET: /
/site_libs/tabwid-1.1.2/tabwid.css (404: Not Found)
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-12-22T08:09:41Z",
"creator": "dmenne",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 3734,
"state": "closed",
"title": "Could not fetch resource site_libs/tabwid-1.1.2/tabwid.css",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3734"
}
|
This issue is based on the discussion in https://github.com/quarto-dev/quarto-cli/discussions/3717. Just reporting here so it's easier to follow.
It would be nice if Quarto supported ANSI colour output with `downlit`. Currently Quarto uses downlit for code linking when `code-link: true`, but this doesn't make colours work.
I thought it would work based on my experiences with `pkgdown`, but after some discussion it sounds like `pkgdown` does some additional processing with `fansi` to support colour output (See https://github.com/quarto-dev/quarto-cli/discussions/3717#discussioncomment-4459352). At this time, if you do need colour output in Quarto, you can get it use the `fansi` knitr hooks for converting ANSI highlighting to HTML highlighting. See https://github.com/quarto-dev/quarto-cli/discussions/3717#discussioncomment-4459352.
One thing that is nice about this approach with `fansi` is that you can turn the hook on and off throughout a document, in case you only want colour output for certain parts. For example, in [this blog post](https://tidytales.ca/posts/2022-12-20_palettes/) I have `fansi` hooks on in the body of the post, but turned them off for the [appendix](https://tidytales.ca/posts/2022-12-20_palettes/#session-info) so the output from `sessioninfo::session_info()` wouldn't be coloured.
If Quarto does support colour output in the future, it would be nice to make it a chunk option (e.g., `colour-output: true/false`) rather than a document-wide option like `code-link` so it can be used selectively when needed.
___
Here's a reprex copied from the discussion that can be used for testing.
````
---
title: "Reprex"
format:
html:
code-link: true
---
```{r}
#| collapse = TRUE
cat(cli::col_red("This is red"), "\n")
cat(cli::col_blue("This is blue"), "\n")
message(cli::col_green("This is green"))
warning(cli::style_bold("This is bold"))
```
````
|
{
"assignee": "cderv",
"comments": 1,
"created_at": "2022-12-22T01:04:10Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3730,
"state": "open",
"title": "Support ANSI colour output with `downlit`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3730"
}
|
### Bug description
I'm trying to run the [example Deno script code](https://quarto.org/docs/projects/scripts.html#deno-scripts) inside a Quarto project (that does have a `_quarto.yml`).
Here's my script, `snel.ts`:
```ts
import { parse } from "https://deno.land/std/encoding/yaml.ts";
const config = parse(Deno.readTextFileSync("_quarto.yml"));
```
When I ran this on Quarto 1.3.21, I got an error:
```
$ quarto run snel.ts
error: Specifier not found in cache: "https://deno.land/[email protected]/encoding/yaml.ts", --cached-only is specified.
at file:///[project path]/snel.ts:1:23
```
I understand that Quarto's Deno can't download modules, but I would assume that this module is one of the cached ones.
I've now upgraded to Quarto 1.3.56, but I'm getting a similar-sounding error:
```
$ quarto run snel.ts
error: Module not found "file:///Users/jgol0005/Applications/quarto/vendor/deno.land/[email protected]/encoding/yaml.ts".
at file:///[project path]/snel.ts:1:23
```
Having a look at the contents of the newly installed Quarto, it looks like the path relative to the Quarto installation should probably be `/bin/vendor/deno-land` rather than `/vendor/deno.land`, although I can't see `encoding/yaml.ts` in any of the cached `std@[version]` directories:
Does Quarto manage filling this cache on demand, or should the full standard library be there on install?
### 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": 16,
"created_at": "2022-12-21T00:21:05Z",
"creator": "jimjam-slam",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 3723,
"state": "closed",
"title": "Can't import std lib module for example Deno script",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3723"
}
|
### Bug description
Hi Quarto-Dev,
I've been kicking the tires on the Confluence publishing feature but I have been unable to push to Confluence due to an `Invalid Confluence parent URL` issue. Is there a regex matcher for Confluence URLs? If so, I'd be happy to try a few pages.
```bash
quarto publish confluence
? Publish with account: βΊ <elided>
? Space or Parent Page URL: βΊ <elided>
ERROR: Invalid Confluence parent URL: <elided>
```
In the above example, I am attempting to use as a parent is a simple page under my Personal Space. I tried with and without spaces and also using the `share link` link version of the page. In all cases the URL fails. Notable, this is a private Atlassian instance so perhaps that is part of the issue?
Thanks,
zach cp
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "allenmanning",
"comments": 3,
"created_at": "2022-12-20T15:21:14Z",
"creator": "zachcp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3720,
"state": "closed",
"title": "ERROR: Invalid Confluence parent URL",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3720"
}
|
### Bug description
quarto 1.3.26, Windows
Cross-referencing tables works for html/docx/pdf when I use `knitr::kable`
It fails for docx (only) for `flextable` and `gt`. `flextable` cross-referencing works in `rmarkdown/knitr`
```
WARNING: Unable to resolve crossref @tbl-mtcars
WARNING: Unable to resolve crossref @tbl-gtcars
```
Similar issues: #1710, #3340
As far I understand #1556, this should work with gh?
````
---
title: "Flextable"
format:
docx
---
## Page references with flextable
```{r}
#| echo: FALSE
#| message: FALSE
#| label: tbl-mtcars
#| tbl-cap: "Motorcars flextable"
mt_head = head(head(mtcars))[,1:5]
flextable::flextable(mt_head)
```
For example, see @tbl-mtcars (does not work for docx, ok for html/pdf)
## Page references with kable
```{r}
#| echo: FALSE
#| message: FALSE
#| label: tbl-kablecars
#| tbl-cap: "Motorcars kable"
knitr::kable(mt_head)
```
For example, see @tbl-kablecars (works for all)
Yihui can do it....
## Page references with gt
```{r}
#| echo: FALSE
#| message: FALSE
#| label: tbl-gtcars
#| tbl-cap: "Motorcars gt chunk captions"
library(gt)
mt_head %>%
gt() %>%
tab_caption(caption = "Motorcars gt code captions")# also ok for html/pdf
```
For example, see @tbl-gtcars (does not work for docx, ok for html/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": null,
"comments": 1,
"created_at": "2022-12-20T15:11:01Z",
"creator": "dmenne",
"is_pull_request": false,
"labels": [
"bug",
"duplicate"
],
"locked": false,
"milestone": null,
"number": 3719,
"state": "closed",
"title": "Unable to resolve crossref in docx tables (works for html/pdf)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3719"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3710
<div type='discussions-op-text'>
<sup>Originally posted by **agerlach** December 19, 2022</sup>
When using `fig-cap` with `fig-subcap` I am getting a weird layout for the main caption with pdf output. `fig-cap` is placed fine when `fig-subcap` is not used. Is this a bug, or am I doing something incorrectly?
````markdown
---
title: Hello World
jupyter: julia-1.8
---
```{julia}
#| echo: false
#| fig-cap: "My Plots"
#| fig-subcap:
#| - "Plot A"
#| - "Plot B"
#| layout-ncol: 2
using Plots
plot(rand(25)) |> display
plot(rand(25)) |> display
```
```{julia}
#| echo: false
#| fig-cap: "My Plots 2"
plot(rand(25)) |> display
```
````
The resulting *.tex contains
```latex
\begin{figure}
\begin{minipage}[t]{0.50\linewidth}
{\centering
\raisebox{-\height}{
\includegraphics{subcap_files/figure-pdf/cell-2-output-1.pdf}
}
\caption{Plot A}
}
\end{minipage}%
%
\begin{minipage}[t]{0.50\linewidth}
{\centering
\raisebox{-\height}{
\includegraphics{subcap_files/figure-pdf/cell-2-output-2.pdf}
}
\caption{Plot B}
}
\end{minipage}%
\newline
\begin{minipage}[t]{0.50\linewidth}
{\centering
My Plots
}
\end{minipage}%
\end{figure}
```
</div>
|
{
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-12-19T15:13:05Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref",
"julia"
],
"locked": false,
"milestone": "v1.4",
"number": 3711,
"state": "open",
"title": "Weird `fig-cap` placement with `fig-subcap` with pdf output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3711"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3704
<div type='discussions-op-text'>
<sup>Originally posted by **cgoo4** December 19, 2022</sup>
When `image:` is left unspecified in a `.qmd` YAML header, the first image found is also used for the listing page. This is great as it avoids specifying the image twice when it's wanted in both the listing and as the feature image for the post.
Could the alternative text from the first image also flow through to the listing page? It would avoid the need to specify this twice, i.e. in the YAML as `image-alt:` and in the inserted image as `fig-alt=`.
Example where specified twice to appear in both the listing and the post: [post in repo](https://github.com/cgoo4/quantumjitter/blob/main/blog/dark/index.qmd)
Example where specified in the first image only and doesn't flow to the listing with the image: [post in repo](https://github.com/cgoo4/quantumjitter/blob/main/project/stories/index.qmd)</div>
|
{
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-12-19T13:28:49Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3706,
"state": "closed",
"title": "Capture `fig-alt=` from the first image for use in the listing page",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3706"
}
|
### Bug description
I'm running quarto 1.2.269 on Windows, using sass files to customize HTML output. It seems that custom theme files for light mode are unexpectedly applied to dark mode.
For example, consider this qmd file:
```md
---
title: Test
format:
html:
theme:
light: [flatly, "custom.scss"]
dark: [darkly]
---
```
and in `custom.scss`:
```scss
/*-- scss:rules --*/
body::after{
content: "foo";
}
```
I expected to get "foo" in light mode only. However, after rendering, "foo" can be seen in both light and dark mode.
I guess this might have something to do with `bootstrap.min.css` and `bootstrap-dark.min.css` included in `<head>`, since both of them are applied in dark mode.
Apologize if I've missed something obvious. 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.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 1,
"created_at": "2022-12-19T12:56:39Z",
"creator": "sun123zxy",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 3705,
"state": "open",
"title": "Custom theme sass file for light mode unexpectedly applied to dark mode",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3705"
}
|
### Bug description
I'm running quarto 1.2.269 on the command line of centos 7. My use-case is to use the same R script to generate multiple reports, and I like to avoid self_contained/embed-resources so users can easily access individual plots etc.
```bash
quarto render '01_heatmaps.rmd' -o 'binarised_v0.0.1-0-ga74c32d.html' -P assay:"binarised"
```
In Rmarkdown the '*_files' would inherit the name of the output, so I'd get something like `binarised_v0.0.1-0-ga74c32d_files`, but in quarto I'm getting `01_heatmaps_files` - so if I attempt to iterate through a set of parametrised reports, I'll over-write the dependencies. In [the documentation](https://quarto.org/docs/output-formats/html-basics.html#self-contained) it says that this is the 'default' behaviour, but I can't find any way of over-riding this default. I don't think I can simply rename the folder, as the links then won't work? Is there a way of reverting the behaviour so that the dependency folder inherits from the output name. Many thanks.
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 1,
"created_at": "2022-12-19T10:46:16Z",
"creator": "macroscian",
"is_pull_request": false,
"labels": [
"bug",
"duplicate"
],
"locked": false,
"milestone": null,
"number": 3703,
"state": "closed",
"title": "'_files' folder not inheriting from output filename set on cli",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3703"
}
|
### Bug description
I just pulled the most recent version of `quarto-cli`, and now all `quarto` commands fail.
For instance, `quarto check` gives the following errors:
```
Check file:///Users/j/Documents/GitHub/quarto-cli/src/quarto.ts
error: TS2554 [ERROR]: Expected 1 arguments, but got 0.
process.kill();
~~~~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/core/process.ts:30:19
An argument for 'signo' was not provided.
kill(signo: Signal): void;
~~~~~~~~~~~~~
at asset:///lib.deno.ns.d.ts:2693:10
TS2339 [ERROR]: Property 'gid' does not exist on type 'typeof Deno'.
return Deno.gid()!;
~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/vendor/deno.land/[email protected]/node/process.ts:637:17
TS2339 [ERROR]: Property 'uid' does not exist on type 'typeof Deno'.
return Deno.uid()!;
~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/vendor/deno.land/[email protected]/node/process.ts:642:17
TS2339 [ERROR]: Property 'uid' does not exist on type 'typeof Deno'.
if (Deno.build.os !== "windows" && info.uid === Deno.uid()) {
~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/vendor/deno.land/[email protected]/node/_fs/_fs_access.ts:33:58
TS2339 [ERROR]: Property 'uid' does not exist on type 'typeof Deno'.
if (Deno.build.os !== "windows" && info.uid === Deno.uid()) {
~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/vendor/deno.land/[email protected]/node/_fs/_fs_access.ts:87:58
TS2339 [ERROR]: Property 'setRaw' does not exist on type 'Reader & ReaderSync & Closer & { readonly rid: number; readonly readable: ReadableStream<Uint8Array>; }'.
Deno.stdin.setRaw(true);
~~~~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/vendor/deno.land/x/[email protected]/ansi/cursor_position.ts:31:14
TS2339 [ERROR]: Property 'setRaw' does not exist on type 'Reader & ReaderSync & Closer & { readonly rid: number; readonly readable: ReadableStream<Uint8Array>; }'.
Deno.stdin.setRaw(false);
~~~~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/vendor/deno.land/x/[email protected]/ansi/cursor_position.ts:34:14
TS2339 [ERROR]: Property 'setRaw' does not exist on type 'Reader & ReaderSync & Closer & { readonly rid: number; readonly readable: ReadableStream<Uint8Array>; }'.
(Deno.stdin.setRaw as setRaw)(
~~~~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/vendor/deno.land/x/[email protected]/prompt/_generic_prompt.ts:299:19
TS2339 [ERROR]: Property 'setRaw' does not exist on type 'Reader & ReaderSync & Closer & { readonly rid: number; readonly readable: ReadableStream<Uint8Array>; }'.
Deno.stdin.setRaw(false);
~~~~~~
at file:///Users/j/Documents/GitHub/quarto-cli/src/vendor/deno.land/x/[email protected]/prompt/_generic_prompt.ts:307:18
Found 9 errors.
```
Iβm running quarto-cli on macOS Ventura 13.1
|
{
"assignee": null,
"comments": 3,
"created_at": "2022-12-17T02:03:05Z",
"creator": "postylem",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3695,
"state": "closed",
"title": "After pulling recent changes, all `quarto` commands fail",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3695"
}
|
### Bug description
Given the following Quarto document:
````markdown
---
title: "test"
---
```{r}
w <- reactable::reactable(iris)
htmlwidgets::saveWidget(
widget = w,
file = "test.html",
selfcontained = TRUE
)
htmltools::includeHTML("test.html")
```
````
When this document is rendered from a terminal (outside RStudio), the R code fails to find Pandoc, producing the error:
```
Quitting from lines 8-18 (index.qmd)
Error in htmlwidgets::saveWidget(widget = w, file = "test.html", selfcontained = TRUE) :
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Calls: .main ... eval_with_user_handlers -> eval -> eval -> <Anonymous>
Execution halted
```
This problem can be avoided by setting `RSTUDIO_PANDOC` to the path to the Pandoc executable included with Quarto:
```bash
RSTUDIO_PANDOC=$QUARTO_ROOT/bin/tools quarto render index.qmd
```
Quarto should set `RSTUDIO_PANDOC` and possibly add its managed Quarto to the PATH.
Using Quarto 1.2.269 on macOS Monterey (12.6.1) and Linux (various versions).
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-12-16T14:40:21Z",
"creator": "aronatkins",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3688,
"state": "closed",
"title": "Help R code discover Pandoc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3688"
}
|
### Bug description
# Main issue
1. **R location is not recognized** while rendering pdf in **VSCode with R** chunks.
2. It is okay if I run the command `quarto_render("~.qmd")` in R terminal in VSCode
3. it is can be partially rendered in Rstudio, Chinese letters are missing
<img width="391" alt="ζͺε±2022-12-16 21 40 03" src="https://user-images.githubusercontent.com/88379522/208110701-4c009328-0384-4a97-a058-0b0a5e584ba0.png">
```
(base) dzhou@bogon homework 1202 quarto % quarto preview "~.qmd" --to pdf --no-browser --no-watch-inputs
ERROR: Error executing '/Applications/R.app/Rscript': No such file or directory (os error 2)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
I do understand that rendering it in Rstudio is more acceptable, but **that can cause another problem, that Chinese letters are not fully rendered** (I'm sure that this can happen for all CJK in Rstudio rendering)
I guess this is a sort of command problem??? that you should only render it in R terminal if there are only R chunks??? I do have no idea for this, running statistics in R and Julia is my best.
# settings
- Quarto 1.2.269 in VSCode
- R 4.2.1, process ID 40651
- macOS Ventura 13.1 (22C65)
**Rstudio** RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 13_1_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
**VSCode** Version: 1.74.1 (Universal)
Commit: 1ad8d514439d5077d2b0b7ee64d2ce82a9308e5a
Date: 2022-12-14T10:33:40.793Z
Electron: 19.1.8
Chromium: 102.0.5005.167
Node.js: 16.14.2
V8: 10.2.154.15-electron.0
OS: Darwin arm64 22.2.0
Sandboxed: No
```
quarto check
[β] Checking Quarto installation......OK
Version: 1.2.269
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.0
Path: /usr/local/bin/python3
Jupyter: 5.1.0
Kernels: julia-1.6, julia-1.7, python3
(|) Checking Jupyter engine render....Traceback (most recent call last):
File "/Applications/quarto/share/jupyter/jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "/Applications/quarto/share/jupyter/notebook.py", line 16, in <module>
import nbformat
ModuleNotFoundError: No module named 'nbformat'
[β] Checking Jupyter engine render....OK
```
Best wishes
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 1,
"created_at": "2022-12-16T13:41:03Z",
"creator": "DerekZ4471",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3687,
"state": "closed",
"title": "R not located while rendering, Quarto VSCode, macOS Ventura",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3687"
}
|
### 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": "cscheid",
"comments": 5,
"created_at": "2022-12-16T10:22:24Z",
"creator": "giabaio",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3686,
"state": "closed",
"title": "fa shortcode broken in navbar?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3686"
}
|
### Bug description
Steps to reproduce:
1. Render the following file.
````
---
title: "MWE"
format: pptx
---
```{r results="asis"}
library(ggplot2)
print(ggplot(mtcars, aes(x = wt)) + geom_histogram())
```
````
Expected output: A Powerpoint document with a title slide and a histogram on the second slide.
Observed output: A Powerpoint document with only a title slide and no histogram.
Note that we get the correct result if we remove `results="asis"`, or if we change format to `html`.
Running on RStudio 2022.07.2 Build 576 within Windows 10.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cderv",
"comments": 8,
"created_at": "2022-12-16T03:01:48Z",
"creator": "Xitian9",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 3683,
"state": "closed",
"title": "ggplot output in \"asis\" R code blocks is not included in Powerpoint output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3683"
}
|
### Bug description
Any content *before* the first Markdown header in a chapter is moved *past* this header when rendered.
## Minimal reproducible example:
1. Create a [new book project](https://quarto.org/docs/books/index.html#quick-start):
```sh
quarto create-project mybook --type book
```
2. Edit the file `mybook/references.qmd` to have the following content:
````md
```{=tex}
\clearpage
\newpage
\listoffigures
\newpage
\listoftables
\newpage
```
# References {.unnumbered}
::: {#refs}
:::
````
3. Render/preview the book:
```sh
quarto preview mybook
```
## Expected result
The default output of a new book project **plus** (in PDF output only) a list of figures and a list of tables immediately *before* the bibliography.
## Actual result
As you will see, the page with the *References* heading will be empty, followed by a page with the list of figures and a page with the list of tables, followed by the bibliography content (the `::: {#refs}` block).
## System details
- Quarto 1.2.280 (issue is also present in latest pre-release v1.3.56)
- Latest TinyTeX providing `XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)`
- Ubuntu 20.04
### 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": 6,
"created_at": "2022-12-15T20:00:37Z",
"creator": "salim-b",
"is_pull_request": false,
"labels": [
"bug",
"wontfix"
],
"locked": false,
"milestone": null,
"number": 3681,
"state": "closed",
"title": "Content *before* first MD header in chapter is moved *past* the header",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3681"
}
|
### Bug description
Rendering a dygraph htmlwidget on quarto document, shows an unexpected scrollbar on right side (and sometimes on bottom part too). It causes impossible to hover over last data point.
It happens on RStudio's Viewer Pane or with web-browsers like Firefox, Chrome or MS-Edge. Not allways with other web-browsers like Falkon or Konqueror.
You can see this issue on [quarto-htmlwidget page](https://quarto.org/docs/interactive/widgets/htmlwidgets.html) or rendering a new document.
I've tried with different figure widths and heights and cannot fix it.
The scrollbar does not appear rendering over a Rmarkdown document
### Reporducible example
```{r}
library(dygraphs)
dygraph(ldeaths, "All Deaths")
```
### Version
- Quarto-cli on OS: 1.2.280
- R Quarto package: 1.2
- RStudio: 2022.07.2.576
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": null,
"comments": 1,
"created_at": "2022-12-15T16:43:17Z",
"creator": "archymedes",
"is_pull_request": false,
"labels": [
"bug",
"duplicate"
],
"locked": false,
"milestone": null,
"number": 3680,
"state": "closed",
"title": "dygraph htmlwidget show unexpected scrollbar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3680"
}
|
### Bug description
Using 1.2.269 on `linux`, `bioconductor_docker`.
`cat /etc/os-release`:
NAME="Ubuntu"
VERSION="20.04.4 LTS (Focal Fossa)"
...
Includes:
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Ubuntu Bionic
Mozilla/5.0 (X11; Linux x86_64; rv:107.0) Gecko/20100101 Firefox/107.0
Consider the following:
1. `_quarto.yml`:
profile:
group:
- [A, B]
2. `index.qmd`:
::: {.content-visible when-profile="A"}
# Print in profile A only
:::
::: {.content-visible when-profile="B"}
# Print in profile B only
:::
3. Call `quarto render --to=pdf --profile=A` or `quarto render --to=pdf --profile=B`
==> all works as expected. Profile specific content rendered as requested.
4. Change `_quarto.yml` to:
project:
type: book
book:
chapters:
- index.qmd
profile:
group:
- [A, B]
5. Call `quarto render --to=pdf --profile=A`
==> all works as expected. Profile specific content rendered as requested.
6. Call `quarto render --to=pdf --profile=B`
==> `quarto` ignores the `.content-visible` stanzas and renders **BOTH**!?
### 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": "jjallaire",
"comments": 6,
"created_at": "2022-12-14T18:05:47Z",
"creator": "r-cheologist",
"is_pull_request": false,
"labels": [
"bug",
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 3673,
"state": "open",
"title": "PDF: Erroneous interaction between project type `book` and `{.content-visible when-profile=\"<PROFILE>\"}`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3673"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3668
<div type='discussions-op-text'>
<sup>Originally posted by **acmuehlhausen-smc** December 14, 2022</sup>
Hey there,
I've got a small but annoying problem designing a reveal.js-presentation in Quarto: when I have slides with no title (e.g.: a contact slide at the end, a slide with a full-size image, a quote ...) it appears in the toc as an empty bullet point, like this:
**TOC**
- Fancy first slide
- On the essence of unicorns
-
How can I get rid of that bullet point? I already tried [this](https://mine-cetinkaya-rundel.github.io/quarto-tip-a-day/posts/23-titleless-slides/) but it only worked for the hamburger menu, not the toc. Some googling showed me a [%notitle] param for reveal.js but I did not find a Quarto implementation for it yet.
Thanks for the help!
Alex</div>
|
{
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-12-14T16:25:53Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 3671,
"state": "open",
"title": "reveal.js presentation: Slides with no title appear in the toc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3671"
}
|
Rendering a dygraph htmlwidget on quarto document, shows an unexpected scrollbar on right side (and sometimes on bottom part too). It causes impossible to hover over last data point.
It happens on RStudio's Viewer Pane or with web-browsers like Firefox, Chrome or MS-Edge. Not allways with other web-browsers like Falkon or Konqueror.
You can see this issue on [quarto-htmlwidget page](https://quarto.org/docs/interactive/widgets/htmlwidgets.html) or rendering a new document.
I've tried with different figure widths and heights and cannot fix it.
The scrollbar does not appear rendering over a Rmarkdown document
- Version Quarto-cli on OS: 1.2.269
- Version R Quarto package: 1.2
- Version RStudio: 2022.07.2.576
```{r}
library(dygraphs)
dygraph(ldeaths, "All Deaths")
```
|
{
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-12-14T16:02:52Z",
"creator": "archymedes",
"is_pull_request": false,
"labels": [
"bug",
"html"
],
"locked": false,
"milestone": "v1.4",
"number": 3894,
"state": "open",
"title": "dygraph htmlwidget show unexpected scrollbar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3894"
}
|
### Bug description
Consider this external file named `mermaid1.mer`:
```
flowchart LR
A
```
When running `Quarto` 1.3.55 on the following script I get `Syntax error in graph, mermaid version 9.1.1`:
````
---
title: "Test"
format:
html:
self-contained: true
---
```{mermaid}
%%| file: mermaid1.mer
```
````
I'm running Ubuntu 22.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-12-13T22:53:23Z",
"creator": "harrelfe",
"is_pull_request": false,
"labels": [
"bug",
"mermaid"
],
"locked": false,
"milestone": "v1.3",
"number": 3665,
"state": "closed",
"title": "Inputting an external mermaid file throws a syntax error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3665"
}
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3658
<div type='discussions-op-text'>
<sup>Originally posted by **GScottAlder** December 13, 2022</sup>
NOTE:
I am using the quarto R package version 1.0 and quarto version 0.9.80
I found the version by running this code: `as.numeric_version(system2(quarto:::find_quarto(), "--version", stdout = TRUE))`
Due to some IT restrictions I have not updated quarto to the most recent release, although I may be able to in the future.
I have multiple *.qmd files that I want to be parameterized. I want them to share parameters and default values by inheriting from a separate YML file.
For example, I have a file named test.qmd with this YML header:
```
---
title: "Test Quarto Report"
metadata-files:
- _params.yml
---
```
Then, in _params.yml I have
```
---
params:
p1: 1.0
p2: "A"
p3: TRUE
---
```
However, this does not work. When I run quarto render, I get an error for "object 'params' not found"
Is there anything I can do to inherit params? Is this not possible in quarto 0.9.80? If so, is it possible in a later release?
Thanks,
Scott
</div>
|
{
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-12-13T21:50:37Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3663,
"state": "open",
"title": "params should work with `metadata-files`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3663"
}
|
Works fine on `ubuntu-latest` just not on `macOS-latest`
Here is the GitHub Action
```
on:
push:
branches: main
name: Setup
jobs:
build-deploy:
runs-on: macOS-latest
steps:
- name: Check out repository
uses: actions/checkout@v3
- name: Set up Quarto
uses: quarto-dev/quarto-actions/setup@v2
with:
# To install LaTeX to build PDF book
tinytex: true
```
Here is the error. `Error: TypeErrorL:`
<img width="985" alt="image" src="https://user-images.githubusercontent.com/2545978/207450678-5d36c236-4e64-44de-b3f3-54bcd19fbdc8.png">
|
{
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-12-13T21:49:10Z",
"creator": "eeholmes",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 3670,
"state": "closed",
"title": "setup.yml: tinytex not installing on macOS-latest",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3670"
}
|
### Bug description
The following example documents the problem. No figure caption or figure number appears unless the first chunk is removed. I'm using Quarto 1.3.55 on Ubuntu 22 and running `quarto render test.qmd`.
````
---
title: "Test"
format:
html:
self-contained: true
---
```{r}
x <- 3
```
```{dot}
//| label: fig-labt
//| fig-cap: "This is a figure caption"
digraph D {
FOO [label="xyz"];
FOO -> {BAR, BAZ};
}
```
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-12-13T18:31:50Z",
"creator": "harrelfe",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3660,
"state": "closed",
"title": "graphviz dot cell ignores figure caption and other info unless it's the first chunk in the script",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3660"
}
|
### Bug description
When rendering book project to pdf, the first sub heading in a chapter is ignored. However, the second subheading is rendered and included in the final pdf file.
The minimal example consists of the following two files.
The `_quarto.qml` file:
```
project:
type: book
book:
title: Test
subtitle: Sub
output-file: test
chapters:
- index.qmd
format:
pdf:
toc: true
toc-depth: 2
keep-tex: true
```
The `index.qmd` file:
```
---
title: "Chapter 1"
---
## Sub Heading
## Sub Heading Again
```
### Expected outcome:
When rendering the document with `quarto render --to pdf`, the document should contain **1.1 Sub Heading** in **Chapter 1**.
### Actual outcome:
The final document does not contain **1.1 Sub Heading**, but instead **1.1 Sub Heading Again** only in **Chapter 1**.
## User Environment
OS: `Ubuntu 20.04.5 LTS`
`quarto check` output:
```
[β] Checking versions of quarto binary dependencies...
Pandoc version 2.19.2: OK
Dart Sass version 1.32.8: OK
[β] Checking versions of quarto dependencies......OK
[β] Checking Quarto installation......OK
Version: 1.3.49
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.6 (Conda)
Path: /home/schroer/mambaforge/envs/quarto/bin/python
Jupyter: 4.11.2
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-12-13T14:37:03Z",
"creator": "jensschroer",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3653,
"state": "closed",
"title": "Book / PDF output: First subheading in a chapter is missing",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3653"
}
|
### Bug description
With quarto 1.3.49 on macOS 11.6, a simple test document with a theorem (https://stackoverflow.com/q/74780867/2777074)
```
---
title: "Untitled"
format: beamer
editor: visual
---
## Quarto
Quarto enables you to weave together content and executable code into a finished presentation. To learn more about Quarto presentations see <https://quarto.org/docs/presentations/>.
::: {#thm-test}
## Just a quick test
:::
```
will lead to a non-compilable document, because you try to define the already defined `theorem` environment. It would be better to check if an environment already exists before you try to define it.
Some other comments about the generated .tex file:
```
% Options for packages loaded elsewhere
\PassOptionsToPackage{unicode}{hyperref}
```
with current hyperref, the unicode option is hardly necessary, it is now the default
```
\PassOptionsToPackage{hyphens}{url}
%
\documentclass[
ignorenonframetext,
```
this will cause problems further down
```
]{beamer}
\usepackage{pgfpages}
```
unnecessary. Even if note pages are shown, beamer will load it automatically
```
\setbeamertemplate{caption}[numbered]
\setbeamertemplate{caption label separator}{: }
\setbeamercolor{caption name}{fg=normal text.fg}
\beamertemplatenavigationsymbolsempty
% Prevent slide breaks in the middle of a paragraph
\widowpenalties 1 10000
\raggedbottom
\setbeamertemplate{part page}{
\centering
\begin{beamercolorbox}[sep=16pt,center]{part title}
\usebeamerfont{part title}\insertpart\par
\end{beamercolorbox}
}
\setbeamertemplate{section page}{
\centering
\begin{beamercolorbox}[sep=12pt,center]{part title}
\usebeamerfont{section title}\insertsection\par
\end{beamercolorbox}
}
\setbeamertemplate{subsection page}{
\centering
\begin{beamercolorbox}[sep=8pt,center]{part title}
\usebeamerfont{subsection title}\insertsubsection\par
\end{beamercolorbox}
}
\AtBeginPart{
\frame{\partpage}
}
\AtBeginSection{
\ifbibliography
\else
\frame{\sectionpage}
\fi
}
\AtBeginSubsection{
\frame{\subsectionpage}
}
\usepackage{amsmath,amssymb}
```
unnecessary, beamer loads them by default
```
\usepackage{lmodern}
\usepackage{iftex}
\ifPDFTeX
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
```
unnecessary, that's the default for several years now
```
\usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
\usepackage{unicode-math}
\defaultfontfeatures{Scale=MatchLowercase}
\defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
\fi
% Use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\IfFileExists{microtype.sty}{% use microtype if available
\usepackage[]{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
\makeatletter
\@ifundefined{KOMAClassName}{% if non-KOMA class
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
\KOMAoptions{parskip=half}}
\makeatother
\usepackage{xcolor}
```
unnecessary, beamer loads it by default
```
\newif\ifbibliography
\setlength{\emergencystretch}{3em} % prevent overfull lines
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}\usepackage{longtable,booktabs,array}
\usepackage{calc} % for calculating minipage widths
\usepackage{caption}
% Make caption package work with longtable
\makeatletter
\def\fnum@table{\tablename~\thetable}
\makeatother
\usepackage{graphicx}
```
unnecessary, beamer loads them by default
```
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
% Set default figure placement to htbp
\makeatletter
\def\fps@figure{htbp}
```
makes no sense in a class without floating mechanism
```
\makeatother
\makeatletter
\makeatother
\makeatletter
\makeatother
\makeatletter
\@ifpackageloaded{caption}{}{\usepackage{caption}}
```
Why? A couple of lines above you force loading the caption package
```
\AtBeginDocument{%
\ifdefined\contentsname
\renewcommand*\contentsname{Table of contents}
\else
\newcommand\contentsname{Table of contents}
\fi
\ifdefined\listfigurename
\renewcommand*\listfigurename{List of Figures}
\else
\newcommand\listfigurename{List of Figures}
\fi
\ifdefined\listtablename
\renewcommand*\listtablename{List of Tables}
\else
\newcommand\listtablename{List of Tables}
\fi
\ifdefined\figurename
\renewcommand*\figurename{Figure}
\else
\newcommand\figurename{Figure}
\fi
\ifdefined\tablename
\renewcommand*\tablename{Table}
\else
\newcommand\tablename{Table}
\fi
}
\@ifpackageloaded{float}{}{\usepackage{float}}
\floatstyle{ruled}
\@ifundefined{c@chapter}{\newfloat{codelisting}{h}{lop}}{\newfloat{codelisting}{h}{lop}[chapter]}
\floatname{codelisting}{Listing}
\newcommand*\listoflistings{\listof{codelisting}{List of Listings}}
\usepackage{amsthm}
```
unnecessary, beamer loads them by default
```
\theoremstyle{plain}
\newtheorem{theorem}{Theorem}[section]
\theoremstyle{remark}
\renewcommand*{\proofname}{Proof}
\newtheorem*{remark}{Remark}
\newtheorem*{solution}{Solution}
\makeatother
\makeatletter
\@ifpackageloaded{caption}{}{\usepackage{caption}}
```
you've already loaded it two times, now three and the next line will also load it
```
\@ifpackageloaded{subcaption}{}{\usepackage{subcaption}}
\makeatother
\makeatletter
\@ifpackageloaded{tcolorbox}{}{\usepackage[many]{tcolorbox}}
\makeatother
\makeatletter
\@ifundefined{shadecolor}{\definecolor{shadecolor}{rgb}{.97, .97, .97}}
\makeatother
\makeatletter
\makeatother
\ifLuaTeX
\usepackage{selnolig} % disable illegal ligatures
\fi
\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
```
hyperref is loaded by default in beamer
```
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
\urlstyle{same} % disable monospaced font for URLs
\hypersetup{
pdftitle={Untitled},
hidelinks,
pdfcreator={LaTeX via pandoc}}
\title{Untitled}
\author{}
\date{}
\begin{document}
\frame{\titlepage}
\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[borderline west={3pt}{0pt}{shadecolor}, enhanced, frame hidden, breakable, interior hidden, boxrule=0pt, sharp corners]}{\end{tcolorbox}}\fi
```
you are loading the beamer class with the ignorenonframetext option. This redefinition will never be seen
```
\begin{frame}{Quarto}
\protect\hypertarget{quarto}{}
Quarto enables you to weave together content and executable code into a
finished presentation. To learn more about Quarto presentations see
\url{https://quarto.org/docs/presentations/}.
\leavevmode\vadjust pre{\hypertarget{thm-test}{}}%
\begin{theorem}[Just a quick test]\label{thm-test}
~
\end{theorem}
\end{frame}
\end{document}
```
(It seems that xelatex is the default engine. Is this really such a good idea? It neither has the speed advantage of pdflatex, nor the goodies of lualatex but comes with a truck load of problems, like missing text on beamer note pages, incorrect uncovering of overlays...)
### 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": "2022-12-13T12:54:41Z",
"creator": "samcarter",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3650,
"state": "open",
"title": "Beamer and theorems",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3650"
}
|
### Bug description
π this is pretty minor to be sure but I also had to narrow down the issue for my own purposes so I thought I would report.
Version of quarto tested on: `v1.0.38`, `v1.2.269` and HEAD here: https://github.com/quarto-dev/quarto-cli/commit/46ce2673bc3a5ce74051c7bc5a4a9c3678e25e7a
I can reproduce on both RStudio* and vscode (quarto extension up to date)
> RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for macOS
> Mozilla/5.0 (Macintosh; Intel Mac OS X 13_0_1) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
I am trying to use plotly with quarto for the first time and I noticed that the modebar hover get buried if one sets `link-external-icon` to `true`:
Obviously I can unblock myself by simply setting it to false which results in this:
However I did have some hope that one could set it on a chunk by chunk basis. Here is a reprex that should reproduce the issue:
````md
---
title: "modebar popup"
format:
html:
link-external-icon: true
execute:
echo: false
warning: false
---
[link](https://www.google.com)
```{r}
library(ggplot2)
library(plotly)
```
```{r}
#| link-external-icon: false
p <- iris |>
ggplot(aes(x = Petal.Width, y = Sepal.Width, text = Species)) +
geom_point()
ggplotly(p)
```
````
Thanks again for such an amazing product!
<details>
<summary>Session Info</summary>
```r
β Session info ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
setting value
version R version 4.2.1 (2022-06-23)
os macOS Ventura 13.0.1
system aarch64, darwin20
ui X11
language (EN)
collate en_CA.UTF-8
ctype en_CA.UTF-8
tz America/Vancouver
date 2022-12-12
pandoc 2.19.2 @ /opt/homebrew/bin/pandoc
β Packages ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
package * version date (UTC) lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
cli 3.4.1 2022-09-23 [1] RSPM (R 4.2.1)
colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
data.table 1.14.6 2022-11-16 [1] RSPM (R 4.2.1)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
digest 0.6.31 2022-12-11 [1] RSPM (R 4.2.1)
dplyr 1.0.10 2022-09-01 [1] RSPM (R 4.2.1)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
ggplot2 * 3.4.0 2022-11-04 [1] RSPM (R 4.2.1)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
gtable 0.3.1 2022-09-01 [1] RSPM (R 4.2.1)
htmltools 0.5.4 2022-12-07 [1] RSPM (R 4.2.1)
htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.0)
httr 1.4.4 2022-08-17 [1] RSPM (R 4.2.1)
jsonlite 1.8.4 2022-12-06 [1] RSPM (R 4.2.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.2.0)
lifecycle 1.0.3 2022-10-07 [1] RSPM (R 4.2.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] RSPM (R 4.2.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
plotly * 4.10.1 2022-11-07 [1] RSPM (R 4.2.1)
purrr 0.3.5 2022-10-06 [1] RSPM (R 4.2.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
rlang 1.0.6 2022-09-24 [1] RSPM (R 4.2.1)
scales 1.2.1 2022-08-20 [1] RSPM (R 4.2.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
tidyr 1.2.1 2022-09-08 [1] RSPM (R 4.2.1)
tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.2.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
vctrs 0.5.1 2022-11-16 [1] RSPM (R 4.2.1)
viridisLite 0.4.1 2022-08-22 [1] RSPM (R 4.2.1)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
```
</details>
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-12-12T21:24:03Z",
"creator": "boshek",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3645,
"state": "closed",
"title": "plotly modebar isn't obscured with link-external-icon: true",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3645"
}
|
# Bug description
With @rlesur we wanted to play with `duckdb` embarked implementation in `observable` notebooks (feature released in Novembre: https://observablehq.com/@observablehq/duckdb)
We tried using CSV and parquet files stored on local file systems. With CSV, everything works fine when using `FileAttachment`. Things are different with `parquet` files.
## Reproducible example
@rlesur proposed a reproducible example [here ](https://git.lab.sspcloud.fr/f7sggu/quarto-ojs-parquet) with a deployed version [there](https://f7sggu.pages.lab.sspcloud.fr/quarto-ojs-parquet/) based on `penguins` dataset.
If you want us to produce an english version because that would help you figuring out what is going on, I can do that.
First, when using ` FileAttachment` with relative link:
~~~
```{ojs}
db = DuckDBClient.of({
penquins: FileAttachment("penguins.parquet")
})
````
~~~
we end up with the following error:
> Error: Invalid Input Error: File 'penguins.parquet' too small to be a Parquet file
@rlesur has had the idea to compare absolute and relative URL in [his notebook](https://git.lab.sspcloud.fr/f7sggu/quarto-ojs-parquet/-/blob/master/index.qmd#L8-47).
With absolute URL it works fine. But relative URL give the same error: https://f7sggu.pages.lab.sspcloud.fr/quarto-ojs-parquet/
I tried to tweak that problem by giving absolute path to `ojs` cell :
~~~
```{python}
import os
path_parquet = os.path.abspath("penguins.parquet")
ojs_define(path = "file:///" + path_parquet)
```
```{ojs}
//| output: false
await db._db.registerFileURL("relative.parquet", path)
```
~~~
but this brought the same error
## Environment
We tried using [quarto v1.3.49](https://github.com/quarto-dev/quarto-cli/releases/tag/v1.3.49) on Linux and Windows OS
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution.
|
{
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-12-12T10:06:51Z",
"creator": "linogaliana",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "v1.3",
"number": 3630,
"state": "closed",
"title": "Read parquet files from local filesystem with duckdb on observable notebooks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3630"
}
|
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