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### Bug description
The following document:
```
---
title: "<div style='zoom:75%;'>min-reprex</div>"
format: html
editor: visual
---
```
yields this warning:
```
pandoc
to: html
output-file: quarto_bug_warning_reprex.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: '<div style=''zoom:75%;''>min-reprex</div>'
editor: visual
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'quarto-input90370470' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".
Output created: quarto_bug_warning_reprex.html
```
HTML tags in the `<h1>` title (within the <body>) are useful, for example, it makes it really easy to add an image above the title, and additional flexibilities of course.
However, quarto yields a warning (and also the html's title is influenced by quarto's behavior).
I suggest that quarto parse html tags and apply them in the body (as it currently does), but for the tab's title (the `<head><title>...</title></head>` use a parsed version without the html tags.
```
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
```
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.36
Path: C:\Program Files\RStudio\bin\quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/PROGRA~1/R/R-42~1.0
LibPaths:
- C:/Users/adisa/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.0/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
| {
"assignee": "dragonstyle",
"comments": 9,
"created_at": "2022-07-29T19:45:26Z",
"creator": "adisarid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1584,
"state": "closed",
"title": "Using html tags in a quarto title document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1584"
} |
Templates are great for their flexibility, but the problem is that the template itself is horrid to look at. Is it possible to come up with a `keep-tex`, perhaps `keep-tex-simplified`, which only includes the *relevant* lines from the template? As in, when it encounters conditional statements in the template, only lines for which the conditional is true are outputted/kept. This would eliminate the clutter from, for example, all of the beamer related code from showing up when I use `keep-tex` on a standard article or vice versa. | {
"assignee": null,
"comments": 3,
"created_at": "2022-07-29T18:06:52Z",
"creator": "tbeason",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1583,
"state": "closed",
"title": "[Feature Request] simplified keep-tex option",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1583"
} |
When I use `Powershell` as my default terminal. After click `Render`, it said
```
cmd /C"F:\Writing\quarto\bin\quarto preview testquarto.qmd --no-browser --no-watch-inputs"
```
and it doesn't work.
I have to manually change `cmd` to `cmd.exe`
```
cmd /C"F:\Writing\quarto\bin\quarto preview testquarto.qmd --no-browser --no-watch-inputs"
```
or use CMD as my default terminal.
| {
"assignee": null,
"comments": 1,
"created_at": "2022-07-29T16:56:37Z",
"creator": "Song921012",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1582,
"state": "closed",
"title": "VScode + Powershell not works",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1582"
} |
I don't think this is currently possible in Quarto but it would be great if there were code block options to add HTML attributes to code blocks and code block output similar to knitr's `class.source`, `class.output` or `attr.source`, `attr.output`. | {
"assignee": null,
"comments": 9,
"created_at": "2022-07-29T16:44:31Z",
"creator": "mivalek",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1581,
"state": "closed",
"title": "FR: add source/output attributes/class option to code blocks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1581"
} |
I'm playing with Quarto Books for the first time having been a R/bookdown user for a while. I have a simple book with two chapters. In the first chapter I define a variable , `x`, and I want to then use `x` in my second chapter. In bookdown this works fine. But with Quarto I get, "Error in eval(expr, envir, enclos) : object 'x' not found" when I click render in RStudio. I'm very willing to accept user error, or that independence of chapters is a design choice. But it wasn't something I was expecting.
I've attached a worked example.
What I'm actually more interesting in working out is how to pass params (from a YAML header) from chapter to chapter. Previously I could include something like this in the index file:
```
---
params:
hello: world
---
```
and then access it in all other chapters
[test_params_quorto.zip](https://github.com/quarto-dev/quarto-r/files/9221802/test_params_quorto.zip)
. | {
"assignee": null,
"comments": 4,
"created_at": "2022-07-29T16:42:45Z",
"creator": "andyofsmeg",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1590,
"state": "open",
"title": "Sharing R environment between book chapters ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1590"
} |
### Bug description
Quarto version: 1.0.37
OS: Windows 10
RStudio: 2022.07.0 Build 548
---
title: "Listing"
author: "Alex"
format: html
---
Listing caption is missing:
```{r}
#| lst-label: lst-first
#| label: lst-second
#| lst-cap: "This is a caption for code listing"
summary(cars)
```
Unable to resolve crossref @lst-first
Unable to resolve crossref @lst-second
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 14,
"created_at": "2022-07-29T16:30:57Z",
"creator": "alex-vinogradov",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 1580,
"state": "open",
"title": "lst-label and lst-cap do not produce listing caption and reference",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1580"
} |
### Bug description
Hello!
I have just installed quarto 1.0.37 and run
`quarto check`
and the output is:
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin
Referenced from: /Applications/quarto/bin/tools/deno (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ____chkstk_darwin
Referenced from: /Applications/quarto/bin/tools/deno (which was built for Mac OS X 10.15)
Expected in: /usr/lib/libSystem.B.dylib
/usr/local/bin/quarto: line 106: 90897 Abort trap: 6 "${SCRIPT_PATH}/tools/deno" ${QUARTO_ACTION} ${QUARTO_DENO_OPTIONS} ${QUARTO_DENO_EXTRA_OPTIONS} "${QUARTO_IMPORT_ARGMAP}" "${QUARTO_TARGET}" "$@"
I have no idea what is going on...
I'm running OsX 10.13.6 on a late 2011 macbook pro i7
Can someone please help?
Thank you in advance
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-29T14:04:24Z",
"creator": "giacombi",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1578,
"state": "open",
"title": "dyld: lazy symbol binding failed: Symbol not found: ____chkstk_darwin",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1578"
} |
### Bug description
I am having problems publishing Quarto documents to Quarto Pub. After creating a basic Quarto website and authenticating my account through the command line, I was able to successfully publish website content to my quartopub.org domain. However, having successfully published a website, I wanted to next attempt publishing a standalone document. I used the RStudio UI (`File > New File > Quarto Document...`) to create a basic Quarto document. I then tried to publish using `quarto publish quarto-pub document.qmd` but it returned the command line error: `ERROR: API Error: 429 (Too Many Requests)`.
**All subsequent efforts to use `quarto publish ...` in the command line, regardless of the file type, have resulted in the same message.** To summarize: I was able to publish a toy example once using the command line, but have not been able to successfully do so again even when using the same procedure.
RStudio: `"Spotted Wakerobin" Release (7872775e, 2022-07-22) for macOS`
OS: `macOS Monterrey 12.4`
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.7 (Conda)
Path: /Users/jacobeliason/opt/anaconda3/bin/python
Jupyter: 4.8.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.1.2
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.1/Resources/library
rmarkdown: 2.12
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "softwarenerd",
"comments": 3,
"created_at": "2022-07-29T12:44:23Z",
"creator": "jcblsn",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1577,
"state": "closed",
"title": "ERROR: API Error: 429 (Too Many Requests)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1577"
} |
Hi all,
I'm working on a relatively heavily customized template for a qmd revealjs presentation (see [here](https://github.com/giabaio/quarto-slides/blob/main/test.qmd)). I think I managed to make things work more or less like I want (there's a slight issue with the logo **in the version I'm sharing** --- I don't understand why... But it works OK everywhere else I used it so that's not the problem).
The problem I can see with `tabset` is that if I use the code
```
include-after: |
<style>
.logo {
background-image: url("assets/images/UCL-stats.png");
background-size: 14% 7%;
background-repeat: no-repeat;
position: absolute;
top: 1.9%; /* 2.65%em */
left: 86%;
height: 100%;
width: 100%;
z-index: 20; !default
}
</style>
<script>
document.querySelectorAll(
'section.slide.level2:not(section.slide.level2.title-slide.center):not(section.slide.level2.nobar)'
)
.forEach(el => {
el.innerHTML += '<div class="logo"></div>';
});
</script>
```
in my `yaml`, which is used to add the logo to the top-right of each slide, then, when I view the presentation on my browser (Firefox), clicking on either of the two tabs brings me back to the title page. If I remove the code above, then the `tabset` works OK and clicking on the tabset's title moves from one to the other.
The other slight issue (not sure whether I'm missing something obvious here, though) is whether you can use the keyboard arrows to navigate through `tabsets`? (I come from `xaringan` and there you can do that so I wondered whether that's a feature that is possible under qmd too?).
Many thanks!
Gianluca | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-29T09:24:31Z",
"creator": "giabaio",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1574,
"state": "open",
"title": "Tabset linking back to first page of presentation?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1574"
} |
I try to make a quarto pptx and hit render. Then PowerPoint tries to open it and says that it detected an error, and it can try to repair. Do you know what the issue is?
| {
"assignee": "cderv",
"comments": 11,
"created_at": "2022-07-28T21:55:52Z",
"creator": "OlexiyPukhov",
"is_pull_request": false,
"labels": [
"needs-repro",
"powerpoint",
"stale"
],
"locked": false,
"milestone": "v1.4",
"number": 1630,
"state": "open",
"title": "Powerpoint asks to repair a pptx quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1630"
} |
When files are missing in extensions (which can happen because of a typo in the filename), our errors are not very informative. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-28T21:24:31Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 1570,
"state": "open",
"title": "Offer better error messages for malformed extensions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1570"
} |
Academic groups would benefit a lot from a listings style that has filtering by author; ideally this would play nicely with our article formats. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-28T20:52:01Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1569,
"state": "open",
"title": "Academic listing style (for list of papers from research group)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1569"
} |
### Bug description
Attempting to publish to Netlify from RStudio Cloud via the RStudio Workbench terminal currently does not work:
```bash
/cloud/project/myblog$ quarto publish netlify
? Authorize (Y/n) βΊ Yes
[403:403:0728/174441.766121:ERROR:ozone_platform_x11.cc(247)] Missing X server or $DISPLAY
[403:403:0728/174441.766172:ERROR:env.cc(226)] The platform failed to initialize. Exiting.
/usr/bin/xdg-open: 869: firefox: not found
/usr/bin/xdg-open: 869: iceweasel: not found
/usr/bin/xdg-open: 869: seamonkey: not found
/usr/bin/xdg-open: 869: mozilla: not found
/usr/bin/xdg-open: 869: epiphany: not found
/usr/bin/xdg-open: 869: konqueror: not found
/usr/bin/xdg-open: 869: chromium: not found
/usr/bin/xdg-open: 869: chromium-browser: not found
[454:454:0728/174441.859915:ERROR:ozone_platform_x11.cc(247)] Missing X server or $DISPLAY
[454:454:0728/174441.859962:ERROR:env.cc(226)] The platform failed to initialize. Exiting.
/usr/bin/xdg-open: 869: www-browser: not found
/usr/bin/xdg-open: 869: links2: not found
/usr/bin/xdg-open: 869: elinks: not found
/usr/bin/xdg-open: 869: links: not found
/usr/bin/xdg-open: 869: lynx: not found
/usr/bin/xdg-open: 869: w3m: not found
xdg-open: no method available for opening 'https://app.netlify.com/authorize?response_type=ticket&ticket=2b3242e1811b5d6fee5970013c7b8a1d'
```
I believe the issue is that quarto is not detecting the RStudio Workbench (Prairie Trillium) environment correctly when quarto is invoked from the terminal. See https://github.com/quarto-dev/quarto-cli/blob/90c7f3ba42ffdae3c2b13ad3d1814f8aaaa14b9f/src/core/platform.ts#L32:L35
The issue may be that the expected ENV vars are not present in the terminal session, so quarto is attempting to open a native browser window which fails due to lacking a display.
```
/cloud/project/myblog$ env | grep RS_
RS_RPOSTBACK_PATH=/usr/lib/rstudio-server/bin/rpostback
RS_SESSION_TMP_DIR=/var/run/rstudio-server/rstudio-rsession
RS_SERVER_RPC_SOCKET_PATH=/var/run/rstudio-server/rstudio-rserver/session-server-rpc.socket
RS_SERVER_LOCAL_SOCKET_PATH=/var/run/rstudio-server/rstudio-rserver/rserver.socket
RS_MONITOR_SOCKET_PATH=/var/run/rstudio-server/rstudio-rserver/rserver-monitor.socket
RS_SERVER_TMP_DIR=/var/run/rstudio-server/rstudio-rserver
```
Example project running on RStudio Cloud:
https://rstudio.cloud/content/4302652
### `quarto check` Output
```block
/cloud/project/myblog$ quarto check
[β] Checking Quarto installation......OK
Version: 1.0.35
Path: /opt/quarto/1.0.35/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.10
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /opt/R/4.2.1/lib/R
LibPaths:
- /cloud/lib/x86_64-pc-linux-gnu-library/4.2
- /opt/R/4.2.1/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
/cloud/project/myblog$ quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 5,
"created_at": "2022-07-28T17:55:54Z",
"creator": "kippandrew",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1567,
"state": "closed",
"title": "Unable to publish to netilfy from RStudio Cloud ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1567"
} |
yaml completion on open string fields should suggest from existing values (a la @kellybodwin's notebooks) | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-28T16:15:49Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"yaml-validation"
],
"locked": false,
"milestone": "Future",
"number": 1566,
"state": "open",
"title": "yaml completion on open string fields should suggest from existing values",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1566"
} |
### Bug description
Typo found in word basics user guide for quarto - the word "may" is repeated in the penultimate paragraph at this web page: [link to page](https://quarto.org/docs/output-formats/ms-word.html )
You **may may** always opt to specify the full name (e.g. atom-one-dark) to bypass this automatic behavior.
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-28T15:59:22Z",
"creator": "higgi13425",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1565,
"state": "closed",
"title": "Typo in word basics user guide for quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1565"
} |
### Bug description
I've got a Jupyterlab notebook that I'm using to write a report. It uses greek letters (in particular ΞΌ). These show up correctly in JupyterLab (and also in the ipynb file if I open it in an editor using utf-8 encoding). However, when quarto converts to a PDF, the ΞΌ character is missing (it appears as a blank) and if I set `keep-tex: true`, the (seemingly utf-8 encoded) `.tex` file includes a different character in place of the ΞΌ: ΒΏ.
I can work round it with things like `$\mu$`, although that puts the ΞΌ in italics (even if I use `\mathrm`), which is undesirable.
I've attached a very simple `.ipynb` file, along with the generated `.tex` and `.pdf` files that are produced when running `quarto render MuTest.ipynb`.
[MuTest.zip](https://github.com/quarto-dev/quarto-cli/files/9208642/MuTest.zip)
I am using Windows 10. I am not using R at all, so haven't ticked the checklist box associated with RStudio.
### `quarto check` Output
```bash
> quarto check
[>] Checking Quarto installation......OK
Version: 1.0.37
Path: C:\Users\ab141979\AppData\Local\Programs\Quarto\bin\
CodePage: unknown
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.7 (Conda)
Path: c:/applications/development/languages/python/python.exe
Jupyter: 4.9.1
Kernels: python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### `quarto tools check` Output
```bash
> quarto tools check
(|) Reading Tool DataSending fatal alert BadCertificate
[>] Reading Tool Data
ERROR: TypeError: error sending request for url (https://api.github.com/repos/yihui/tinytex-releases/releases/latest): error trying to connect: invalid peer certificate contents: invalid peer certificate: UnknownIssuer
```
(this is probably due to the corporate zscaler proxy, which replaces SSL certificates and generally makes things difficult...)
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- N/A documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2022-07-28T11:08:44Z",
"creator": "abudden",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1559,
"state": "closed",
"title": "UTF-8 Characters not rendering properly in latex output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1559"
} |
In VSCode-Quarto, the autocomplete is available for div block, but this seems not available in RStudio. Is this something that could be supported for RStudio?
VSCode-Quarto
RStudio
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-28T09:32:18Z",
"creator": "Fred-Wu",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1558,
"state": "open",
"title": "No autocomplete for div block in RStudio",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1558"
} |
For now you have to choose a single kernel, right? I think running multi-language notebooks would be great. E.g. I use a lot of Julia but still do most of my plotting in R.
There are different possibilities, e.g. using multiple kernels (R, Julia, Python) to run their respective cells or alternatively using thing like Julia RCall [1] to run `{r}` cells or PyCall [2] to run `{python}` cells. The second option would make it much easier to pass objects between different languages.
[1] https://github.com/JuliaInterop/RCall.jl
[2] https://github.com/JuliaPy/PyCall.jl | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-28T09:26:57Z",
"creator": "gdkrmr",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1557,
"state": "closed",
"title": "Can I use multiple languages in the same notebook?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1557"
} |
### Bug description
#### Description
When rendered via Quarto with output format as docx, caption (tbl-cap) and crossref (@tbl-ref) not working with flextable.
#### Reproducible example
````
---
title: Flextable in Word
format: docx
---
# Tables
Reference @tbl-flextable
```{r}
#| label: tbl-flextable
#| tbl-cap: "Caption 2"
library(flextable)
flextable(head(mtcars))
```
````
See output docx file: [mwe_book.docx](https://github.com/quarto-dev/quarto-cli/files/9205320/mwe_book.docx)
This issue is also mentioned here on flextable github page: <a href="https://github.com/davidgohel/flextable/issues/385#issuecomment-1196280019">flextable Github page</a>
#### Expected result
Caption and crossref should render correctly in Word doc
#### RStudio information
```bash
$long_version
[1] "2022.02.3+492"
$release_name
[1] "Prairie Trillium"
```
#### OS information
Windows 10 Enterprise
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 0.9.649
Path: C:\Program Files\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/PROGRA~1/R/R-42~1.0
LibPaths:
- C:/Users/username/Documents/R/win-library/4.2
- C:/Program Files/R/R-4.2.0/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 24,
"created_at": "2022-07-28T04:30:20Z",
"creator": "leeroyaus",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 1556,
"state": "open",
"title": "Captions & crossrefs not rendering in Quarto with Flextable",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1556"
} |
### Bug description
Trying to use Plot.dodgeX in a ojs cell and getting the following error when I render to HTML:
Here's a simple example that produces the error when I render:
```{ojs}
testd = [
{
n: "bob",
y: "1",
c: "a"
},
{
n: "bob",
y: "2",
c: "b"
},
{
n: "jane",
y: "3",
c: "a"
},
{
n: "jane",
y: "0",
c: "b"
},
]
```
```{ojs}
Plot.plot({
facet: {
data: testd,
x: "c",
},
marks: [
Plot.frame(),
Plot.dotY(
testd,
Plot.dodgeX({
y: "y",
fill: "n",
anchor: "middle"
})
)
]
})
```
Running exact same cells in an Observable notebook produces the expected plot:
Note I tried to upload the example in a .qmd file but github says it does not support uploads with that extension!
I'm running Windows 10 Enterprise
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.36
Path: C:\Users\sjordan\AppData\Local\Programs\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.4
Path: C:/Python310/python.exe
Jupyter: 4.11.1
Kernels: python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/PROGRA~1/R/R-42~1.0
LibPaths:
- C:/Users/sjordan/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.0/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed v2022.07 v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-07-27T21:16:53Z",
"creator": "stuvjordan-uroc",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "Future",
"number": 1553,
"state": "closed",
"title": "\"TypeError: Plot.dodgeX is not a function\" using Plot.dodgeX in quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1553"
} |
I believe the error message
https://github.com/quarto-dev/quarto-cli/blob/9aab5bdb83ae567b4a38c9374a58412dea41a8de/src/core/jupyter/capabilities.ts#L76
is confusing, because an environment variable with the name `QUARTO_JUPYTER` does not exist. I think it should be called `QUARTO_PYTHON` because that is the name of the variable that is checked in the code at
https://github.com/quarto-dev/quarto-cli/blob/9aab5bdb83ae567b4a38c9374a58412dea41a8de/src/core/jupyter/capabilities.ts#L56 | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-27T16:18:36Z",
"creator": "asmaier",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1551,
"state": "closed",
"title": "Env variable QUARTO_JUPYTER does not exist",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1551"
} |
I tried to integrate a quarto revealjs presentation into a quarto document as an iframe like
```
---
title: "test"
format: html
---
<iframe src="https://quarto.org/docs/presentations/revealjs/demo/" width="210px" height="120px"></iframe>
```
When rendering this document the content of the slides is scaled correctly, but the menu button, footer text, logo and slide number stay too big and overlap the content:
I think it would be better if the scaling of the menu button, footer text, logo and slide number would follow the scaling of the content. | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-27T14:32:00Z",
"creator": "asmaier",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1547,
"state": "open",
"title": "Odd scaling of footer, logo and slide number for presentation in iframe",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1547"
} |
### Bug description
Hi,
I think I encountered a bug when using `ojs_define` and transposing a data frame for plotting with `ojs`.
If any value in the data frame is 0 then the value will become `undefined` after transposing.
MWE:
````md
---
title: transpose bug
---
```{r}
ojs_define(df = data.frame(a = 0, b = 1))
```
```{ojs}
df
```
```{ojs}
transpose(df)
```
````
The output from the first `ojs` cell is as expected:
```
Object {
a: Array(1) [0]
b: Array(1) [1]
}
```
The second cell after transposing converts the original 0 to `undefined`
```
Array(1) [
0: Object {a: undefined, b: 1}
]
```
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.37
Path: redacted
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.12 (Conda)
Path: redacted
Jupyter: 4.10.0
Kernels: julia-1.7, python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.0.5
Path: redacted
LibPaths:
- redacted
rmarkdown: 2.7
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-27T13:37:27Z",
"creator": "p-gw",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1546,
"state": "closed",
"title": "transpose introduces undefined values",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1546"
} |
The following binaries and one shared lib can be reduces in size if stripped:
* `bin/tools/dart-sass/sass` (9.6 MB -> 4.8 MB)
* `bin/tools/deno`(86 MB -> 62 MB)
* `bin/tools/deno_dom/libplugin.so` (4.7 MB -> 1.3 MB)
βΉοΈ `bin/tools/esbuild` (7.8 MB) and `bin/tools/pandoc` (78 MB) are already stripped. | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-27T12:40:47Z",
"creator": "benz0li",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1545,
"state": "open",
"title": "Strip binaries and shared libs in `bin/tools` to reduce size",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1545"
} |
Could the cover image be used by default as image for Quarto books?
And if one could input alternative text #1543 could it be used as image-alt? | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-07-27T10:28:53Z",
"creator": "maelle",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1544,
"state": "open",
"title": "Use cover as Twitter image for Quarto books by default?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1544"
} |
I'd like to be able to input alternative text for the cover image. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-27T06:52:15Z",
"creator": "maelle",
"is_pull_request": false,
"labels": [
"bug",
"accessibility"
],
"locked": false,
"milestone": "v1.1",
"number": 1543,
"state": "closed",
"title": "Could one input alternative text for the cover image of a Quarto book?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1543"
} |
[code-server](https://github.com/coder/code-server) [sets environment variable VSCODE_PROXY_URI](https://github.com/coder/code-server/issues/1510). | {
"assignee": "jjallaire",
"comments": 5,
"created_at": "2022-07-27T05:23:52Z",
"creator": "benz0li",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1542,
"state": "closed",
"title": "[Quarto Extension] Base preview/serve URL on `VSCODE_PROXY_URI` if existent",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1542"
} |
I love the [variables](https://quarto.org/docs/authoring/variables.html#var) feature and am using it all over my websites. I'm getting it to work in some parts of the `_quarto.yml` file, but not all.
For example, I am using `repo` in my `_variables.yml` file stores the url to a Github repo. In the footer, I can use `{{< var repo >}}` and it replaces `{{< var repo >}}` with the url, but it won't render if I put it in the navbar like this:
```r
- icon: github
href: "{{< var repo >}}"
```
I just get the text `{{< var repo >}}` instead of the replaced text. | {
"assignee": "dragonstyle",
"comments": 11,
"created_at": "2022-07-26T19:57:05Z",
"creator": "jhelvy",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 1627,
"state": "closed",
"title": "project level `_variables.yml` not rendering in navbar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1627"
} |
Should the following be: https://github.com/quarto-dev/quarto-web/blob/70505935652e59a629cac5af541cbfd7f093f1e4/docs/extensions/_formats-common.qmd#L49-L52
- if shared:
```
contributes:
format:
common:
format-resources:
- plos2015.bst
```
- or if specific to, for example, pdf format:
```
contributes:
format:
pdf:
format-resources:
- plos2015.bst
```
From the current documentation, it's not that easy to understand what this is exactly for.
A directory tree structure and/or a Quarto document showing that the files in `format-resources` are copied to the root of the directory (at least in theory, see https://github.com/quarto-dev/quarto-cli/issues/1538) and thus can be used from within the Quarto document could clarify the interesting part of that feature. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-07-26T19:28:10Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1633,
"state": "closed",
"title": "`format-resources` wrong format in yaml? (and documentation suggestion)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1633"
} |
From https://github.com/mcanouil/quarto-revealjs-coeos/issues/4, kind of thanks to @cderv I discovered an issue with the mechanism behind `format-resources`.
Everything listed in format-resources for a given format should be copied every time, but that's not at all the case.
## TL;DR
Repository: https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli-1538
## Details
<details><summary>See some details</summary>
Let's define a fake template with some resources explicitly stated for each formats:
```yaml
title: Coeos Presentation Template
author: MickaΓ«l CANOUIL
version: 1.0.0
contributes:
formats:
html:
format-resources:
- setup-ggplot2-coeos.R
- about.qmd
- cover.jpg
pdf:
format-resources:
- setup-ggplot2-coeos.R
- about.qmd
- cover.jpg
```
Now, let's have a simple Quarto document:
````md
---
title: "A Title"
subtitle: "A Subtitle"
author: MickaΓ«l Canouil, *Ph.D.*
format: demo-html
---
# Introduction
```{r}
source("setup-ggplot2-coeos.R")
```
{{< include about.qmd >}}
````
</details>
## Issues
- In PDF and HTML: `{{< include about.qmd >}}` does not trigger a copy thus a "not found" error.
- In PDF and HTML: `source("setup-ggplot2-coeos.R")` does not trigger a copy thus a "not found" error.
- In PDF: `` triggers a copy of all resources (even when the other two are not called/used).
- In HTML: `` does not trigger a copy leading again to a "not found" error. | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-07-26T18:57:37Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1538,
"state": "closed",
"title": "[Quarto Extension] `format-resources` not properly detected and copied in both HTML and PDF formats",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1538"
} |
It would be great to generate the automatically documentation for the CLI options on `quarto-web`. Ideally, we'd do it in the same way that we do the documentation for yaml options, by deferring to a single source of truth. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-25T19:53:52Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"documentation",
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1531,
"state": "open",
"title": "Automatically generate `quarto-web`-ready documentation from Cliffy command descriptions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1531"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1521
<div type='discussions-op-text'>
<sup>Originally posted by **edavidaja** July 25, 2022</sup>
currently I'm using a reveal presentation with `theme: night` and adding
`%%{init: {"theme": "dark" } }%%`
to each diagram. I'm not sure if this works for every diagram type--the mermaid website suggests that theming, for example, state machines has to be done via a different mechanism.</div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-25T18:49:35Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1530,
"state": "open",
"title": "Automatically set mermaid themes to match dark / light",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1530"
} |
### Bug description
The following is on an M1 Mac.
I had an Rmd document which following this great blog post [here](https://www.andrewheiss.com/blog/2021/08/27/tikz-knitr-html-svg-fun/#connecting-dvisvgm-to-ghostscript-on-macos), includes tikz code chunks which produce dvi files, which are converted to svg files with `dvisvgm` (which is simply obtained with `tinytex::tlmgr_install('dvisvgm')`).
On macOS, for the dvi to svg conversion, it is required to provide the `dvisvgm` executable with the path to the dynamically linked Ghostscript library libgs.dylib.
I naively installed Ghostscript using Homebrew with a simple `brew install ghostscript`. On aarch64 R under `rmarkdown::render(...)` the calls to `dvisvgm` worked as I expected but when I tried to render the document using Quarto the calls to `dvisvgm` failed.
I found that the *libgs.dylib* from the Homebrew installation was only for the arm64 architecture.
```
$ file /opt/homebrew/Cellar/ghostscript/9.56.1/lib/libgs.dylib.9.56
/opt/homebrew/Cellar/ghostscript/9.56.1/lib/libgs.dylib.9.56: Mach-O 64-bit dynamically linked shared library arm64
```
I then obtained a full Ghostscript installation from the pkg installer from [here](https://pages.uoregon.edu/koch/) which has both architectures.
```
$ file /usr/local/share/ghostscript/9.56.1/lib/libgs.dylib.9.56
/usr/local/share/ghostscript/9.56.1/lib/libgs.dylib.9.56: Mach-O universal binary with 2 architectures: [x86_64:Mach-O 64-bit dynamically linked shared library x86_64
- Mach-O 64-bit dynamically linked shared library x86_64] [arm64]
/usr/local/share/ghostscript/9.56.1/lib/libgs.dylib.9.56 (for architecture x86_64): Mach-O 64-bit dynamically linked shared library x86_64
/usr/local/share/ghostscript/9.56.1/lib/libgs.dylib.9.56 (for architecture arm64): Mach-O 64-bit dynamically linked shared library arm64
```
Linking to this dylib meant the calls to `dvisvgm` ran as expected under Quarto.
I was wondering if it is worth mentioning somewhere in the docs that the architecture of linked dylibs currently can't just be arm64 (until I guess you have an arm64 version of Quarto).
An example Qmd file is as below.
````rmd
---
title: "Example for dylib architecture issue"
format: gfm
---
```{r setup, include=FALSE}
require('tinytex')
if (!tinytex::check_installed('dvisvgm')) tinytex::tlmgr_install('dvisvgm')
```
* Call to `dvisvgm` with the arm64 dylib. In its output this is missing the
`ps` row to show the dylib has been linked.
```{r}
system2(
'dvisvgm',
c(
'--libgs=/opt/homebrew/Cellar/ghostscript/9.56.1/lib/libgs.dylib.9.56',
'-l'
),
stdout = TRUE
)
```
* Using the dylib including both architectures produces the expected output.
```{r}
system2(
'dvisvgm',
c(
'--libgs=/usr/local/share/ghostscript/9.56.1/lib/libgs.dylib.9.56',
'-l'
),
stdout = TRUE
)
```
````
It produces
````
Example for dylib architecture issue
================
- Call to `dvisvgm` with the arm64 dylib. In its output this is
missing the `ps` row to show the dylib has been linked.
``` r
system2(
'dvisvgm',
c(
'--libgs=/opt/homebrew/Cellar/ghostscript/9.56.1/lib/libgs.dylib.9.56',
'-l'
),
stdout = TRUE
)
```
[1] "bgcolor background color special"
[2] "color complete support of color specials"
[3] "dvisvgm special set for embedding raw SVG snippets"
[4] "em line drawing statements of the emTeX special set"
[5] "html hyperref specials"
[6] "papersize special to set the page size"
[7] "pdf PDF hyperlink, font map, and pagesize specials"
[8] "tpic TPIC specials"
- Using the dylib including both architectures produces the expected
output.
``` r
system2(
'dvisvgm',
c(
'--libgs=/usr/local/share/ghostscript/9.56.1/lib/libgs.dylib.9.56',
'-l'
),
stdout = TRUE
)
```
[1] "bgcolor background color special"
[2] "color complete support of color specials"
[3] "dvisvgm special set for embedding raw SVG snippets"
[4] "em line drawing statements of the emTeX special set"
[5] "html hyperref specials"
[6] "papersize special to set the page size"
[7] "pdf PDF hyperlink, font map, and pagesize specials"
[8] "ps dvips PostScript specials"
[9] "tpic TPIC specials"
````
### `quarto check` Output
```
(base) toms-Mac-mini:~ tom$ quarto check
[β] Checking Quarto installation......OK
Version: 0.9.649
Path: /Applications/RStudio.app/Contents/MacOS/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.12 (Conda)
Path: /Users/tom/opt/miniconda3/bin/python
Jupyter: 4.10.0
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/tom/Library/R/arm64/4.2/library
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/site-library
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
(/) Inspecting toolsDownload https://deno.land/x/[email protected]/directories.ts
(|) Inspecting toolsDownload https://deno.land/x/[email protected]/deps.ts
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-25T16:57:49Z",
"creator": "remlapmot",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "Future",
"number": 1526,
"state": "closed",
"title": "[Suggestion] Document when using Quarto on M1 Macs that linked `dylib`s to executables need to be both (or maybe just x86_64?) architectures",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1526"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1509
<div type='discussions-op-text'>
<sup>Originally posted by **jmgirard** July 23, 2022</sup>
Sometimes when I run `quarto publish gh-pages`, it hangs (i.e., gets stuck) on "Preparing worktree."
* branch gh-pages -> FETCH_HEAD
Rendering for publish:
...
branch 'gh-pages' set up to track 'origin/gh-pages'.
HEAD is now at 2054a64 Built site for gh-pages
Preparing worktree (resetting branch 'gh-pages'; was at 2054a64)
Any ideas how to troubleshoot, fix, or prevent this?</div> | {
"assignee": "cderv",
"comments": 9,
"created_at": "2022-07-25T15:19:35Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.2",
"number": 1524,
"state": "closed",
"title": "Git hangs on preparing worktree with `quarto publish gh-pages` on windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1524"
} |
Hello!
I love using Quarto and I am constantly amazed by the new features I discover daily. In the interest of advancing open source features, would it be possible to create a library on the Quarto website (or elsewhere) of user-generated Quarto extensions and shortcodes? Currently, it seems the only way to find user-generated extensions is to search around GitHub and hope developers have tagged their projects accordingly. A centralized library would be great for discovering new open source content and inspiring additional projects.
Thanks! | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-25T14:58:39Z",
"creator": "noah-silver",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1523,
"state": "open",
"title": "[Feature Request] Quarto Extensions Library",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1523"
} |
### Bug description
Loading functions from either from local JS/WASM files or from observablehq notebooks has stopped working quarto-1.0.36 macos r4.2.0
Consider the following code, which loads the `rand` function from `@ljcolling/rand` and then makes runs it on a button press
```{ojs}
import {rand} from "@ljcolling/rand"
```
```{ojs}
mutable d = null
```
```{ojs}
{
return d === null ? null : d["m"].map((v) => v.x);
}
```
```{ojs}
viewof clicked = Inputs.button("Click me")
```
```{ojs}
{
if (clicked) {
mutable d = rand(1, 1, 10, 10);
}
}
```
Clicking the button results in the following error:
```
OJS Error
TypeError: rand is not a function
```
However, this code works as expected with no errors when rendering with quarto-0.9.163 or on the observablehq website (https://observablehq.com/@ljcolling/ojs-bug)
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.36
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.12
Path: /usr/local/opt/[email protected]/bin/python3.9
Jupyter: 4.9.1
Kernels: python3
(\) Checking Jupyter engine render....2022-07-24 15:48:15,105 - traitlets - WARNING - Kernelspec name python3 cannot be found!
No such kernel named python3
[β] Checking Jupyter engine render....OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-07-24T14:53:42Z",
"creator": "ljcolling",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "Future",
"number": 1513,
"state": "closed",
"title": "Externally loaded JS/WASM functions stopped working in ojs blocks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1513"
} |
Crossref syntax such as `See @fig-demofiglabel` is not well supported with no-space situation for `docx` output format.
```
WARNING: Unable to resolve crossref @fig-demofiglabelζη€Ί
```
For example:
```
ε¦@fig-demofiglabelζη€Ί
```
I tried the syntax below, with no success
```
ε¦@{fig-demofiglabel}ζη€Ί
```
## MWE
````
---
title: MWE
format: docx
---
See @fig-demofiglabel
ε¦@{fig-demofiglabel}ζη€Ί
If I add a space before`@`, it works.
ε¦ @{fig-demofiglabel}ζη€Ί
```{r}
#| label: fig-demofiglabel
#| fig-cap: "Demo figure"
plot(1)
```
````
<img width="596" alt="Screenshot 2022-07-23 at 22 08 56" src="https://user-images.githubusercontent.com/3145794/180608635-124557c7-a459-4c43-9ea9-dfbaec009ac0.png">
| {
"assignee": null,
"comments": 5,
"created_at": "2022-07-23T13:44:11Z",
"creator": "mingsu",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1507,
"state": "open",
"title": "Crossref syntax not well supported with `non-space-sperated` situation ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1507"
} |
### Bug description
Embedding HTML inside of book does not seem to work.
In the root of my project directory I have :
1. a quarto file called test1.qmd that contains
````r
---
title: "test1"
---
```{r}
#| echo: false
knitr::include_url({"x.html"})
```
````
2. a YAML file called _quarto.yml that contains:
````yml
project:
type: book
title: "test"
book:
title: "CSS Notes"
author: "Me"
date: "7/22/2022"
chapters:
- index.qmd
- test1.qmd
format:
html:
theme: cosmo
````
3. a html file called x.html that contains
```html
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta http-equiv="X-UA-Compatible" content="ie=edge">
<title>What is CSS?</title>
<link rel="stylesheet" href="style.css">
</head>
<body>
<div class="container">
<img src="./img/image.jpeg">
<div class="content">
<h3>Where is my rUM?</h3>
<button>Click Here</button>
</div>
</div>
</body>
</html>
```
4. a css file called style.css that contains
```css
.container {
width: 400px;
margin: auto;
background: #eee;
position: absolute;
top: 30%;
left: 50%;
transform: translate(-50%, -50%);
border-radius: 5px 5px 0 0;
box-shadow: 5px 7px 15px #ccc;
}
.container img {
width: 100%;
border-radius: 5px 5px 0 0;
}
.content {
padding: 10px;
text-align: center;
font-family: sans-serif;
}
.content h3 {
color: #777;
}
.content button {
padding: 10px 20px;
margin-bottom: 10px;
background: coral;
font-size: 15px;
color: #fff;
outline: none;
border-radius: 20px;
border: none;
box-shadow: 3px 5px 10px #ccc;
transition: all .2s;
}
.content button:hover {
background: orangered;
}
```
5. an empty index.qmd file
6. a child directory called img containing an image file called image.jpeg
When I click Render Book in the Build tab of RStudio IDE the book renders. The content of the embedded page appears without the image or the ccs styling. The Background Jobs tab tells me
```
Watching files for changes
Browse at http://localhost:7932/
GET: /
GET: /test1.html
GET: /x.html
/style.css (404: Not Found)
/img/image.jpeg (404: Not Found)
```
If I remove the `type: book` line from the YAML file ... :
````yml
project:
title: "test"
book:
title: "CSS Notes"
author: "Me"
date: "7/22/2022"
chapters:
- index.qmd
- test1.qmd
format:
html:
theme: cosmo
````
... and click Render on the test1.qmd file, the page renders showing the image and using the CSS.
Is this a bug or am I botching the syntax somewhere (or doing something else wrong)?
I am running RStudio IDE: 2022.07.0 Build 548 on macOS Monterey Version 12.4.
I can do a show and tell at RStudio::conf if it helps....
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.35
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.9
Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3
Jupyter: 4.11.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Up to date v2022.07 v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-23T13:35:50Z",
"creator": "RaymondBalise",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1506,
"state": "open",
"title": "CSS and images from embedded HTML inside a Quarto book do not render",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1506"
} |
Currently, no document has mentioned the customization of `figurename` and `tablename` in quarto documents.
I have tried to follow the same as in `Rmarkdown` syntax, but it failed at least for `LaTeX` engine.
For pdf output, the `figurename` and `tablename` were reset by `crossrefMetaInject()` in `crossref.lua` even I add `figurename` and `tablename` option in `YAML`.
```
function crossrefMetaInject()
return {
Meta = function(meta)
metaInjectLatex(meta, function(inject)
inject(usePackage("caption"))
inject(
"\\AtBeginDocument{%\n" ..
maybeRenewCommand("contentsname", param("toc-title-document", "Table of contents")) ..
maybeRenewCommand("listfigurename", listOfTitle("lof", "List of Figures")) ..
maybeRenewCommand("listtablename", listOfTitle("lot", "List of Tables")) ..
maybeRenewCommand("figurename", titleString("fig", "Figure")) ..
maybeRenewCommand("tablename", titleString("tbl", "Table")) ..
"}\n"
)
if latexListings() then
inject(
"\\newcommand*\\listoflistings\\lstlistoflistings\n" ..
"\\AtBeginDocument{%\n" ..
"\\renewcommand*\\lstlistlistingname{" .. listOfTitle("lol", "List of Listigs") .. "}\n" ..
"}\n"
)
else
inject(
usePackage("float") .. "\n" ..
"\\floatstyle{ruled}\n" ..
"\\@ifundefined{c@chapter}{\\newfloat{codelisting}{h}{lop}}{\\newfloat{codelisting}{h}{lop}[chapter]}\n" ..
"\\floatname{codelisting}{" .. titleString("lst", "Listing") .. "}\n"
)
inject(
"\\newcommand*\\listoflistings{\\listof{codelisting}{" .. listOfTitle("lol", "List of Listings") .. "}}\n"
)
end
local theoremIncludes = theoremLatexIncludes()
if theoremIncludes then
inject(theoremIncludes)
end
end)
return meta
end
}
end
``` | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-23T09:38:07Z",
"creator": "mingsu",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1504,
"state": "closed",
"title": "How to customize the `figurename` and `tablename`?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1504"
} |
I have a blog post with a description that contains inline r (to estimate reading time)
it renders nicely for the post itself
but not in the listing page!
here's the yml of my post's index.qmd:
```
---
draft: false
title: A nice blog post
description: |
Reading time: `r ifelse(file.size("index.qmd")/2000 <= 1, '<1 minute', paste0(round(file.size("index.qmd")/2000), ' minutes'))`
---
```
Any idea of how I can fix the listing? | {
"assignee": null,
"comments": 6,
"created_at": "2022-07-23T03:01:48Z",
"creator": "harrig12",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1505,
"state": "open",
"title": "inline R in blog yaml isn't executed on listing page",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1505"
} |
Is it necessary to write release notes for the released version? It is not easy to know what bugs have been fixed.
https://github.com/quarto-dev/quarto-cli/releases/tag/v1.0.36 | {
"assignee": "dragonstyle",
"comments": 10,
"created_at": "2022-07-23T02:01:46Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1503,
"state": "closed",
"title": "Release Notes?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1503"
} |
### Bug description
Computationally generated tables from python do not display properly in HTML.
Minimal qmd file:
````md
---
title: "Untitled"
---
## Quarto
```{python}
#| label: tbl-planets
#| tbl-cap: Planets
from IPython.display import Markdown
from tabulate import tabulate
table = [["Sun",696000,1989100000],
["Earth",6371,5973.6],
["Moon",1737,73.5],
["Mars",3390,641.85]]
Markdown(tabulate(
table,
headers=["Planet","R (km)", "mass (x 10^29 kg)"],
tablefmt="pipe"
))
```
````
Produces this output:
Job output:
```bash
/bin/bash: /home/susan/.local/share/r-miniconda/envs/r-reticulate/lib/libtinfo.so.6: no version information available (required by /bin/bash)
/bin/bash: /home/susan/.local/share/r-miniconda/envs/r-reticulate/lib/libtinfo.so.6: no version information available (required by /bin/bash)
processing file: test.qmd
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: tbl-planets (with options)
List of 3
$ engine : chr "python"
$ original.params.src: chr "python"
$ chunk.echo : logi FALSE
|......................................................................| 100%
ordinary text without R code
output file: test.knit.md
pandoc
to: html
output-file: test.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: Untitled
Output created: test.html
Watching files for changes
Browse at http://localhost:5844/
```
Rstudio version information: First tried on
```
RStudio
2022.02.3 Build 492
Β© 2009-2022 RStudio, PBC
"Prairie Trillium" Release (1db809b8, 2022-05-20) for Ubuntu Bionic
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
```
but also holds when I upgrade to the latest preview release:
```
RStudio
2022.07.0 Build 548
Β© 2009-2022 RStudio, PBC
"Spotted Wakerobin" Release (34ea3031, 2022-07-06) for Ubuntu Bionic
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
```
OS information: Ubuntu 21.10
### `quarto check` Output
```bash
(base) susan@Ralph:~/Projects/test$ quarto check
[β] Checking Quarto installation......OK
Version: 1.0.35
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.13 (Conda)
Path: /home/susan/.local/share/r-miniconda/envs/r-reticulate/bin/python
Jupyter: 4.11.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/susan/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
(base) susan@Ralph:~/Projects/test$ quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 17,
"created_at": "2022-07-22T17:04:47Z",
"creator": "srvanderplas",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1501,
"state": "closed",
"title": "Teach reticulate to understand IPython methods",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1501"
} |
The default quarto template for beamer doesn't have a footer. If one selects a beamer theme with footer, the logo isn't placed in the footer (like in revealjs) but above the footer line. This would still be ok, but the logo is not scaled correctly. It seems to be inserted in original size. Instead it should be scaled relative to text size in the footer (as done for revealjs). It would be nice if at least quartos default theme for beamer would support a footer with logo similar to revealjs. That would make converting a revealjs presentation to beamer easier and generate more predictable results. At the moment the best way to convert a quarto revealjs presentation to pdf is not using beamer, but instead use https://revealjs.com/pdf-export/ . | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-22T16:21:40Z",
"creator": "asmaier",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1499,
"state": "open",
"title": "Support for logo and footer in beamer output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1499"
} |
In my opinion it doesn't make sense to present footnotes at the bottom of a slide in a presentation. Not only do they often cause issues with the layout because there is simply not enough space for them on the slide. It also doesn't make sense to show footnotes which cannot be read by the viewer anyway, because the fontsize is so small. Also in presentations I use footnotes mostly just as replacement for citations, because for a presentation I do not want to deal with a second file just for a very small bibliography.
That said, I was happy to see that - although it is not documented at https://quarto.org/docs/presentations/revealjs/#asides-footnotes - it is possible to move footnotes to the end of a quarto presentation with
```
---
title: "Some presentation"
format:
revealjs:
reference-location: document
beamer:
reference-location: document
section-title-footnotes: References
---
```
However there are several issues with that:
1. It doesn't work for beamer
2. In revealjs clicking on a footnote number navigates you to the title page, but not to the footnote at the end of the document (But the hover shows the content of the footnote nicely). The footnote link is somehow messed up.
3. The footnotes at the end of the document are missing a backlink to the footnote.
4. It seems to me that although the footnote is not shown on the slide, adding a footnote to a slide can still break the layout. For example in the following presentation the image on the `middle` slide will appear much smaller than on the `start` side. The reason is the footnote:
```
---
title: "Some presentation"
format:
revealjs:
reference-location: document
section-title-footnotes: References
---
## start
- text without footnote
## middle
- text with footnote^[important footnote]
## end
```
Changing the layout if a footnote is present makes sense, if the footnotes are on the same slide, but it shouldn't be done if the footnotes are collected at the end of the document.
| {
"assignee": null,
"comments": 2,
"created_at": "2022-07-22T15:28:17Z",
"creator": "asmaier",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "Future",
"number": 1498,
"state": "open",
"title": "Presentations + Footnotes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1498"
} |
### Bug description
In a new project, this is the reprex document
````
---
title: "Untitled"
format:
html:
self-contained: false
---
## Title
```{r}
mtcars |>
kableExtra::kbl()
```
````
This will error with latest **htmltools** 0.5.3 version:
````
#> Error in `normalizePath()`:
#> ! path[1]="test_files\libs/kePrint-0.0.1": Le chemin dβaccΓ¨s spΓ©cifiΓ© est introuvable
#> Backtrace:
#> β
#> 1. ββglobal .main()
#> 2. ββexecute(...)
#> 3. ββpandoc_includes(...)
#> 4. ββdependencies_from_render(input, files_dir, knit_meta, format)
#> 5. ββhtml_dependencies_as_string(extras$dependencies, files_dir)
#> 6. ββbase::lapply(dependencies, htmltools::copyDependencyToDir, files_dir)
#> 7. ββhtmltools (local) FUN(X[[i]], ...)
#> 8. ββbase::normalizePath(target_dir, "/", TRUE)
#> Warning messages:
#> 1: In dir.create(outputDir) :
#> cannot create dir 'test_files\libs', reason 'No such file or directory'
#> 2: In dir.create(target_dir) :
#> cannot create dir 'test_files\libs\kePrint-0.0.1', reason 'No such file or directory'
#> Execution halted
````
Note that with 0.5.2 version, the warning are still there
```
#> Warning messages:
#> 1: In dir.create(outputDir) :
#> cannot create dir 'test_files\libs', reason 'No such file or directory'
#> 2: In dir.create(target_dir) :
#> cannot create dir 'test_files\libs\kePrint-0.0.1', reason 'No such file or directory'
```
This is because the directory passed to `copyDependencyToDir` for `test.qmd` is `test_files/libs` which is not really supported in **htmtools** I believe. I opened an issue there to discuss: https://github.com/rstudio/htmltools/issues/331
Quick fix in quarto would be to create `test_files/` folder ourself, but v1 is already out, so this can wait and we could see in **htmltools** can support it IMO.
| {
"assignee": null,
"comments": 1,
"created_at": "2022-07-22T13:37:57Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1497,
"state": "closed",
"title": "Quarto with R does not correctly use htmltools for dependency creation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1497"
} |
Thank you for developing Quarto! I'm not sure which repo to post this issue in; I am posting it here as I'm working with Quarto in RStudio, but I apologize if it is the wrong repo.
According to [the Quarto website](https://quarto.org/docs/authoring/title-blocks.html#custom-backgrounds) we can set up a custom background for a title block banner by using the image path as an argument for `title-block-banner` in the header. Also according to [the website](https://quarto.org/docs/output-formats/html-basics.html#self-contained), we can use `self-contained: true` under `html` to create "a standalone HTML file with no external dependencies", "with images, CSS, etc. embedded into the HTML file". But when I create a supposedly self-contained HTML file with a banner image, I need to keep the HTML file in the root directory of the provided image path; otherwise, the image doesn't show. In other words, the document is not self-contained, inasmuch as it depends on the presence of the image file. | {
"assignee": null,
"comments": 12,
"created_at": "2022-07-22T06:52:46Z",
"creator": "GilHenriques",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1496,
"state": "open",
"title": "Self-contained HTML with block banner figure",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1496"
} |
Not sure if this is a bug as I may be doing something wrong, so not creating an issue yet. Windows and RStudio info are copied at bottom.
Setup:
- I have an RStudio project with multiple subfolders for different elements of the project
- one subfolder is for a reveal.js presentation I am preparing
- this subfolder has its own _quarto.yml file, and an index.qmd file with the presentation
- when I render the presentation subfolder it creates the presentation in a sub-subfolder called _site
- the presentation looks fine if I double-click its index.html file locally, or if I upload the _site folder to netlify.app manually
Issue:
- I am signed into my netlify account in Chrome, which is also my default browser
- (just to be safe, I repeated this signed into my netlify account in Edge, in case Windows did something to prevent Chrome being the proper default browser, but I get the same result)
- in RStudio, if I open a terminal and cd to the presentation subfolder and then enter in the terminal `quarto publish netlify` it asks me to authorize
- after entering "Y" it tries to do something, but all that happens is that it opens my "Documents" folder in Windows Explorer (i.e, in the file manager) and does not upload the site
- as an experiment, I then tried creating my own _publish.yml file with the proper site id and url. It then asks me if I want to update that site, and I say yes; it then asks for authorization to which I say yes; after which it again opens my Documents folder in Windows Explorer and does not upload the site
Is it possible that I am doing something wrong? Obviously it is not a major issue as I can upload the presentation _site folder manually, but it would be nice to do it with a one-line terminal command. Would appreciate advice. Many thanks.
Edition Windows 11 Pro
Version 22H2
Installed on β5/β13/β2022
OS build 22622.436
Experience Windows Feature Experience Pack 1000.22632.1000.0
RStudio 2022.07.1+551 "Spotted Wakerobin" Release (a1f594a0dbfd7d23a9ba3115277c474bd8642212, 2022-07-08) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36 | {
"assignee": null,
"comments": 6,
"created_at": "2022-07-21T23:35:36Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1490,
"state": "closed",
"title": "quarto publish netlify does not seem to work on my Windows 11 machine",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1490"
} |
Hello, when I tried to sign up for Quarto Pub with GitHub here, https://quartopub.com/sign-up, I was first taken to the GitHub landing page to approve access to my GitHub account, but following that the page does not allow me to sign in. Is signing in with GitHub enabled at this time? | {
"assignee": "softwarenerd",
"comments": 3,
"created_at": "2022-07-21T21:39:47Z",
"creator": "gvelasq",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1525,
"state": "open",
"title": "Unable to sign up for Quarto Pub with GitHub",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1525"
} |
### Bug description
(via @emilhvitfeldt.) We found this ΒΏbug? where the size of an image/plot depends on the presence of (potential empty) speaker notes for revealjs slides. reprex: https://emilhvitfeldt.github.io/notes-image-sizing/
reprex: https://github.com/EmilHvitfeldt/notes-image-sizing/blob/main/index.qmd
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 99.9.9
Path: /Users/cscheid/repos/github/quarto-dev/quarto-cli/package/dist/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.12
Path: /Users/cscheid/venvs/3_9_5/bin/python3
Jupyter: 4.7.1
Kernels: julia-1.7, python3, c
(|) Checking Jupyter engine render....Exception ignored in: <function BaseEventLoop.__del__ at 0x105cee430>
Traceback (most recent call last):
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/base_events.py", line 688, in __del__
self.close()
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/unix_events.py", line 58, in close
super().close()
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/selector_events.py", line 87, in close
self._close_self_pipe()
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/selector_events.py", line 94, in _close_self_pipe
self._remove_reader(self._ssock.fileno())
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/selector_events.py", line 272, in _remove_reader
key = self._selector.get_key(fd)
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 191, in get_key
return mapping[fileobj]
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 72, in __getitem__
fd = self._selector._fileobj_lookup(fileobj)
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 226, in _fileobj_lookup
return _fileobj_to_fd(fileobj)
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 42, in _fileobj_to_fd
raise ValueError("Invalid file descriptor: {}".format(fd))
ValueError: Invalid file descriptor: -1
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Up to date 869685 869685
tinytex Up to date v2022.07 v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-21T20:41:12Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1487,
"state": "closed",
"title": "revealjs: size of an image depends on the presence of (potential empty) speaker notes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1487"
} |
### Bug description
Long tables generated by `kableExtra` are created using the `tabu` environment (rather than `tabular`) and the captions are incorrect (the LaTeX code generated includes a subcaption and the caption from the YAML `tbl-cap` instruction is missing.
````markdown
---
title: "MWE"
format: pdf
keep-tex: true
---
```{r}
#| label: tbl-test1
#| echo: false
#| tbl-cap: "Table caption"
data("mtcars")
knitr::kable(mtcars[1:5,],
row.names = FALSE)
```
```{r}
#| label: tbl-test2
#| echo: false
#| tbl-cap: "Table caption"
knitr::kable(mtcars[1:5,],
row.names = FALSE) |>
kableExtra::kable_styling(full_width = TRUE)
```
```{r}
#| label: tbl-test3
#| echo: false
#| tbl-cap: "Table caption"
data("mtcars")
kableExtra::kbl(mtcars[1:5,],
row.names = FALSE)
```
````
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.35
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.5
Path: /usr/bin/python3
Jupyter: 4.11.1
Kernels: python3, julia-1.6, sagemath
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib64/R
LibPaths:
- /home/lbelzile/R/x86_64-pc-linux-gnu-library/4.2
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```{bash}
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
I have `tinytex` version 0.40 installed. `chromium` is also installed on my computer.
```
tinytex::tlmgr_version()
tlmgr revision 63068 (2022-04-18 07:58:07 +0200)
TeX Live (https://tug.org/texlive) version 2022
```
Running Arch Linux
```
RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for Ubuntu Bionic
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
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-21T19:36:00Z",
"creator": "lbelzile",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1486,
"state": "open",
"title": "quarto treats tables from `kableExtra` (`tabu`) as subtables",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1486"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1484
<div type='discussions-op-text'>
<sup>Originally posted by **dhicks** July 21, 2022</sup>
I'm working on a project that includes, in effect, an extensive Mermaid tutorial. I'd like to set all of the Mermaid blocks to `echo: true`. Either setting `echo: true` in `_quarto.yml` doesn't seem to do the trick or I'm confused about where to put it. Non-working example attached.
[_quarto.yml.zip](https://github.com/quarto-dev/quarto-cli/files/9162064/_quarto.yml.zip)
</div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-21T19:32:56Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1485,
"state": "closed",
"title": "Change project-wide execution options for Mermaid",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1485"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1482
<div type='discussions-op-text'>
<sup>Originally posted by **tbeason** July 21, 2022</sup>
There is some discussion on the Quarto guide about how to use various environments from R or Python. Right now, it seems that in order to use Julia code blocks I must keep any packages that I want to use in my global/default environment, rather than project specific ones. In Julia, this done by having a `Project.toml` file for the project (and perhaps a `Manifest.toml` also but not always needed).
When starting Julia you can call `julia --project=Project.toml` if it is in the current directory or you can start Julia normally and from the REPL type `]` and then `activate .`
```julia
] activate .
```
or you can write
```julia
using Pkg
Pkg.activate(".")
```
I know that the last option would work if I added it to a (each?) code block, but is there a way to just add something to the `quarto.yml` file instead to use a `Project.toml` file for the whole project?
</div> | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2022-07-21T15:36:38Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"julia"
],
"locked": false,
"milestone": "Future",
"number": 1483,
"state": "open",
"title": "Julia project specific environments (Project.toml)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1483"
} |
Dear Quarto dev-team,
I've got a small feature requests that I hope are is correctly adressed here. Though, I am not sure if this is an issue with Quarto rather than RStudio. In any case, thanks for your amazing work. I really like working with Quarto.
## Save cookie preferences in RStudio
Is there a way to save the cookie preferences in RStudio? It is a tad annoying to close the pop-up window while editing (and re-rendering) a blog post. | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-21T12:56:25Z",
"creator": "AlbertRapp",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1480,
"state": "open",
"title": "Small feature requests for editing blog posts",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1480"
} |
### Bug description
This is a bit odd behavior: Brackets as in `{ggplot2}` are not rendered properly on a listings page if included in a title. But this only happens if a title ends with a word in brackets. I've tried escaping the brackets with `\` or `\\` but that did not help.
### Reprex
I've taken a standard default blog and tweaked a blog post's title a bit. You can find it in the following repo:
https://github.com/AlbertRapp/curly-brackets-blog-issue
### RStudio version
"Prairie Trillium" Release (1db809b8, 2022-05-20) for Ubuntu Bionic
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 version
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 99.9.9
Path: /home/albert/quarto-cli/package/dist/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.10
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/albert/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
### `quarto tools check` Output
```bash
(|) Inspecting toolsCheck file:///home/albert/quarto-cli/src/resources/vendor/deno-land/x/puppeteer@9-0-2/mod.ts
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-21T12:47:59Z",
"creator": "AlbertRapp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1479,
"state": "closed",
"title": "Blog listings page don't include a title's last word if it is written in {}",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1479"
} |
### Bug description
I am not sure if this is a Quarto problem or a Netlify problem. But I'm giving it a try here anyway:
On my blog's landing page, I want to add a bit of custom scss-code to this one specific page. I have done that by including
```
---
page-layout: full
header-includes: |
<link href="index-styles.scss" rel="stylesheet">
---
```
in the YAML-header. This works out nicely when I render my blog within RStudio. But once I publish my blog on Netlify, the changes in `index-styles.scss` are ignored. But I've checked: The header of the landing page still includes `<link href="index-styles.scss" rel="stylesheet">`.
### RStudio version
"Prairie Trillium" Release (1db809b8, 2022-05-20) for Ubuntu Bionic
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 version
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 99.9.9
Path: /home/albert/quarto-cli/package/dist/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.10
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/albert/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
### `quarto tools check` Output
```bash
(|) Inspecting toolsCheck file:///home/albert/quarto-cli/src/resources/vendor/deno-land/x/puppeteer@9-0-2/mod.ts
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-21T12:39:04Z",
"creator": "AlbertRapp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1478,
"state": "closed",
"title": "file-specific scss-file is not used after publishing on Netlify",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1478"
} |
## Context
We currently configure our tex environment to include the template directory in the search path when compiling LaTeX to PDF. We do this in `latexmk.ts:65-71`:
````typescript
// Resolve any tex input paths
const texInputDirs: string[] = format.pandoc.template
? [`${dirname(format.pandoc.template)}//`]
: [];
if (format.render[kLatexInputPaths]) {
texInputDirs.push(...format.render[kLatexInputPaths]!);
}
````
This was originally to allow templates to refer to TeX assets and those references to be resolved in the template folder. But we have since introduced `format-resources` and would rather than supporting assets be copied adjacent to the `tex` file so manually compiling the file will work correctly and without additional configuration.
## Issue
If you provide a LaTeX template, and a `tex` file in that LaTeX template's folder (recursively) has the same name as an intermediary file using during PDF compilation, that file will be used. For example, in this directory structure:
```
foo/
template.qmd
template.tex
_extensions/
my-extension/
template.tex <--- this will be used when compiling the PDF! :(
```
If the extension in the above case provides `template.tex` as a LaTeX template, that template will be used instead of the `template.tex` file sitting adjacent to the `qmd` file.
| {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-07-21T00:17:03Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1474,
"state": "closed",
"title": "Incorrect TeX search paths cause erratic behavior with conflicting `.tex` files",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1474"
} |
### Bug description
If the following slide displays text below the plot, setting a pause in front of the plot will push the text off the screen (page1).
````qmd
---
title: sample
format:
revealjs: default
engine: knitr
---
## page1
foo
. . .
```{r}
plot(mtcars)
```
bar
## page2
foo
```{r}
plot(mtcars)
```
bar
````
### `quarto check` Output
```sh
[β] Checking Quarto installation......OK
Version: 1.0.35
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.10
Path: /usr/bin/python3
Jupyter: 4.10.0
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.0
Path: /usr/local/lib/R
LibPaths:
- /usr/local/lib/R/site-library
- /usr/local/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-07-20T15:59:11Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1471,
"state": "open",
"title": "Revealjs: Rows entering after the pause are ignored by the plot size and pushed out of the screen",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1471"
} |
{
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-07-20T15:39:49Z",
"creator": "t-kalinowski",
"is_pull_request": false,
"labels": [
"enhancement",
"websites"
],
"locked": false,
"milestone": "Future",
"number": 1470,
"state": "open",
"title": "FR: Websites automatically detect user preference for dark mode from OS",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1470"
} |
|
The following document:
````markdown
---
title: Test123
---
```{python}
#| label: tbl-planets
#| tbl-cap: Planets
from IPython.display import Markdown
from tabulate import tabulate
table = [["Sun",696000,1989100000],
["Earth",6371,5973.6],
["Moon",1737,73.5],
["Mars",3390,641.85]]
Markdown(tabulate(
table,
headers=["Planet","R (km)", "mass (x 10^29 kg)"]
))
```
````
Should produce a captioned, numbered, striped table. Instead it produces an unnumbered, uncaptioned, plain table. Note that DOM structure is a little different than I was expecting as I was thinking it would be contained in a div.cell. | {
"assignee": "jjallaire",
"comments": 0,
"created_at": "2022-07-20T12:12:45Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "1.0",
"number": 1466,
"state": "closed",
"title": "Incorrect Table Output from Computational Table",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1466"
} |
### Bug description
Currently, using Python and Quarto supposes that `py.exe` is used.
First Python is check on windows with py launcher if `PY_PYTHON` is set
https://github.com/quarto-dev/quarto-cli/blob/e13e08c7e0036f42b6e3e1f77ad16ef1d4d20ff5/src/core/jupyter/capabilities.ts#L34-L37
But also a second time if conda not found
https://github.com/quarto-dev/quarto-cli/blob/e13e08c7e0036f42b6e3e1f77ad16ef1d4d20ff5/src/core/jupyter/capabilities.ts#L44-L51
Using `pyenv` on windows (https://pyenv-win.github.io/pyenv-win/) will not register python version in registry so `py.exe` will not found it.
Here is my setup
````powershell
> py --list
Installed Pythons found by C:\Windows\py.exe Launcher for Windows
No Installed Pythons Found!
> pyenv versions
* 3.9.13 (set by C:\Users\chris\scoop\apps\pyenv\current\pyenv-win\version)
> quarto check jupyter
[>] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
> (Get-Command python3).Path
C:\Users\chris\scoop\apps\pyenv\current\pyenv-win\shims\python3.bat
> python3 C:\Users\chris\Documents\DEV_R\quarto-cli\src\resources\capabilities\jupyter.py
versionMajor: 3
versionMinor: 9
versionPatch: 13
versionStr: "3.9.13 (tags/v3.9.13:6de2ca5, May 17 2022, 16:36:42) [MSC v.1929 64 bit (AMD64)]"
conda: false
execPrefix: "C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13"
executable: "C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13/python3.exe"
jupyter_core: 4.11.1
nbformat: 5.4.0
nbclient: 0.6.6
ipykernel: 6.15.1
````
So for now `quarto` does not find Python because `py.exe` does not find it.
Current workaround is to set `QUARTO_PYTHON`
```powershell
$env:QUARTO_PYTHON=$(pyenv which python3)
```
Then
````powershell
> quarto check jupyter
[>] Checking Python 3 installation....OK
Version: 3.9.13
Path: C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.13/python3.exe
Jupyter: 4.11.1
Kernels: bash, julia-1.7, python3
[>] Checking Jupyter engine render....OK
````
I think it would be helpful to bring better support to pyenv for windows inside Quarto.
As a side note, this below does not found `python` binary on windows even if in PATH
https://github.com/quarto-dev/quarto-cli/blob/e13e08c7e0036f42b6e3e1f77ad16ef1d4d20ff5/src/core/jupyter/capabilities.ts#L41-L42
because of Deno limitation on Windows (same as tinytex fixes) and `requireQuoting()` with `safeWindowsExec()` is required to make it work.
This would however prevent finding `python3` which is looked after.
Anyway, I think there is some improvement to do here for Windows user experience. | {
"assignee": "cderv",
"comments": 1,
"created_at": "2022-07-20T09:29:53Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"windows",
"python-setup"
],
"locked": false,
"milestone": "Future",
"number": 1463,
"state": "open",
"title": "Support other python on Windows than py.exe supported ones (like pyenv)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1463"
} |
### Bug description
Quarto is ignoring `warning: false` passed to knitr.
Consider the minimal working example:
`_quarto.yml`:
```
project:
title: "mwe"
editor: visual
```
`mwe.qmd`:
``````
---
title: "mwe"
---
## Quarto
```{r}
#| output: asis
#| warning: true
warning("My warning with warning: true")
```
```{r}
#| output: asis
#| warning: false
warning("My warning with warning: false")
```
``````
It produces
For comparison, consider the minimal working example in R Markdown:
``````
---
title: "mwe"
author: "Raniere Silva"
date: "2022-07-20"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r output='asis', warning=TRUE}
warning("My warning with warning: true")
```
```{r output='asis', warning=FALSE}
warning("My warning with warning: false")
```
``````
The R Markdown document produces
## Environment
Operating System: Ubuntu
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.32
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.5 (Conda)
Path: /opt/conda/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
[β] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /opt/conda/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-20T05:01:18Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1462,
"state": "open",
"title": "Support knitr warning option",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1462"
} |
### Bug description
I'm building an extension for formatting my thesis at Oxford. Let's say I have the following bare-bones extension:
```yaml
title: Oxford Thesis Format
author: Benjamin Lee
version: 0.1.0
contributes:
format:
pdf:
format-resources:
- ociamthesis.cls
```
When I render the PDF on my Mac, it works _but_ the .cls file isn't cleaned up as would be expected.
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.28
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.13
Path: /usr/local/opt/[email protected]/bin/python3.9
Jupyter: 4.8.1
Kernels: corona, python3, squiggle, deep-rules, condo, julia-1.0, viroids, python37564bit620d0d3e6fc64febbcdac4f79a1dc46f, hla, mechwolf, krtd, javascript, krtd-binning
(\) Checking Jupyter engine render....dyld[45896]: Library not loaded: @executable_path/../.Python
Referenced from: /Users/BenjaminLee/.virtualenvs/corona/bin/python3.7
Reason: tried: '/Users/BenjaminLee/.virtualenvs/corona/bin/../.Python' (no such file), '/usr/local/lib/.Python' (no such file), '/usr/lib/.Python' (no such file)
Kernel died before replying to kernel_info
[β] Checking Jupyter engine render....OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2022-07-19T20:35:28Z",
"creator": "Benjamin-Lee",
"is_pull_request": false,
"labels": [
"bug",
"early-in-release"
],
"locked": false,
"milestone": "v1.4",
"number": 1460,
"state": "open",
"title": "format-resources are not cleaned up after rendering",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1460"
} |
### Bug description
panel-tabset does not work when I create the tabs/headings using a for loop and display a matplotlib chart under each heading. For example:
```{python}
from IPython.display import display, Markdown
import matplotlib.pyplot as plt
```
::: {.panel-tabset}
```{python}
for i in ["tab1 inside for loop", "tab2 inside for loop"]:
display(Markdown(f"\n# {i}:\n"))
fig = plt.figure()
ax = fig.add_subplot(111)
plt.show()
```
:::
Gives the following output, with no tabs:
In contrast, if the tabs/headings are not created inside a for loop the output is correct, with the tabs as expected:
::: {.panel-tabset}
### tab1 no for loop
```{python}
fig = plt.figure()
ax = fig.add_subplot(111)
```
### tab2 no for loop
```{python}
fig = plt.figure()
ax = fig.add_subplot(111)
```
:::
And if I create the tabs/headings inside a for loop, but only display text, the output is correct:
::: {.panel-tabset}
```{python}
for i in ['tab1 for loop no figure', 'tab2 for loop no figure']:
display(Markdown(f"\n# {i}:\n"))
display(Markdown("testing text"))
```
:::
My problem is that I would like to display matplotlib charts inside tabs, but the number of tabs depends on the input data and can vary. Currently that does not seem to be possible.
I'm using Windows 10.
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.32
Path: C:\Program Files\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.5
Path: C:/Users/kylie/AppData/Local/Programs/Python/Python310/python.exe
Jupyter: 4.11.1
Kernels: python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.1.0
Path: C:/PROGRA~1/R/R-41~1.0
LibPaths:
- C:/Users/kylie/Documents/R/win-library/4.1
- C:/Program Files/R/R-4.1.0/library
rmarkdown: 2.11
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [x] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-19T13:46:01Z",
"creator": "kylie-foster",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1456,
"state": "open",
"title": "panel-tabset not working with for loop that displays matplotlib charts",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1456"
} |
### Bug description
Switching the website theme is not triggering a change in the scrollbar color.
https://user-images.githubusercontent.com/4706822/179755369-406956c0-7d85-442a-aa6b-b789fa94b30f.mov
The problem only happens in Safari.
In a website project we have customized the navbar color using the scss variable `$navbar-bg` using different colors for light and the dark theme eg:
In the `_quarto.yml` we have:
```
format:
html:
theme:
light: [flatly, light.scss]
dark: [darkly, dark.scss]
```
`light.scss` and `dark.scss` both set the `$navbar-bg` with:
```
/*-- scss:defaults --*/
$navbar-bg: #e83e18;
```
Here's a test repository that can be used to reproduce the issue: https://github.com/dfalbel/test-navbar
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.32
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.13 (Conda)
Path: /Users/dfalbel/Library/r-miniconda/envs/r-reticulate/bin/python
Jupyter: 4.10.0
Kernels: 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
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-07-19T13:01:47Z",
"creator": "dfalbel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1455,
"state": "closed",
"title": "Scrollbar keeps color when switching themes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1455"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1451
<div type='discussions-op-text'>
<sup>Originally posted by **andrewpbray** July 19, 2022</sup>
Version 4.2.0 of revealjs implemented a feature that allows you to specify the line number on which a code chunk will start. I don't see it as a must-have feature, but it'd be helpful when displaying more than one chunk of code from the same file.
Description of feature: https://revealjs.com/code/#line-number-offset-4.2.0
Changelog: https://github.com/hakimel/reveal.js/releases/tag/4.2.0 | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-19T08:56:16Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1454,
"state": "open",
"title": "[FR] Support line number offset for code blocks in revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1454"
} |
### Bug description
Below are three chunks: diagram with mermaid, diagram with dots, figure with R code.
```` markdown
```{mermaid}
%%| echo: fenced
%%| label: fig-mermaid
%%| fig-width: 2
%%| fig-cap: A caption that contains words like use, or, and.
flowchart LR
A[A] --> B(B)
A[A] --> C(C)
```
```{dot}
//| echo: fenced
//| label: fig-dot
//| fig-width: 2
//| fig-cap: A caption that contains words like use, or, and.
graph G {
layout=neato
a -- b;
a -- c;
}
```
```{r}
#| echo: fenced
#| label: fig-r
#| fig-width: 6
#| fig-cap: A caption that contains words like use, or, and.
plot(cars)
```
````
The syntax highlighting in the output is inconsistent across these chunks -- comments seem to receive highlighting like code in the diagram chunks.
<img width="805" alt="Screen Shot 2022-07-19 at 2 10 09 AM" src="https://user-images.githubusercontent.com/5965649/179677963-73b4258b-e24b-411e-8256-5c44acd6feeb.png">
<img width="800" alt="Screen Shot 2022-07-19 at 2 10 16 AM" src="https://user-images.githubusercontent.com/5965649/179677982-174bd8a0-fdea-4548-b1a3-c091b3918dde.png">
<img width="803" alt="Screen Shot 2022-07-19 at 2 10 24 AM" src="https://user-images.githubusercontent.com/5965649/179677992-fd36e247-36a5-434f-bfc1-3e2aee009431.png">
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.32
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.1
Path: /usr/local/bin/python3
Jupyter: 4.9.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/mine/Desktop/RStudio/quarto-tip-a-day/renv/library/R-4.2/x86_64-apple-darwin17.0
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Up to date v2022.07 v2022.07
```
- RStudio: RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_4_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
- OS: macOS 12.4
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-19T06:12:41Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1453,
"state": "open",
"title": "Issues with syntax highlighting for code comments in diagram chunks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1453"
} |
### Bug description
Include the following in a Quarto document:
```` markdown
```{mermaid}
%%| echo: true
flowchart LR
A[Hard edge] --> B(Round edge)
B --> C{Decision}
C --> D[Result one]
C --> E[Result two]
```
````
In the output, there is a blank line at the top of the code chunk.
<img width="1348" alt="Screen Shot 2022-07-19 at 12 36 03 AM" src="https://user-images.githubusercontent.com/5965649/179666034-32e7a95a-0ded-43d3-ab48-ab774c997685.png">
This happens with `echo: fenced` as well.
<img width="1342" alt="Screen Shot 2022-07-19 at 12 36 44 AM" src="https://user-images.githubusercontent.com/5965649/179666049-38678eee-0236-4d82-bb84-49d11cde82e3.png">
And also with `dot` chunks.
- RStudio: RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_4_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
- OS: macOS 12.4
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.32
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.1
Path: /usr/local/bin/python3
Jupyter: 4.9.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/mine/Desktop/RStudio/quarto-tip-a-day/renv/library/R-4.2/x86_64-apple-darwin17.0
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Up to date v2022.07 v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-07-19T04:42:37Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1452,
"state": "closed",
"title": "Blank line when `echo: true` and `echo: fenced` with mermaid and dot chunks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1452"
} |
The introduction of custom formats has caused an additional regression on partial completions.
Minimal reproduction:
```
---
format:
html:
c_ # <- complete from cursor in "_"
---
```
yields a different completion set from:
```
---
format:
html:
_ # <- complete from cursor in "_"
---
```
The issue is we're confusing the context in which partial completions should be allowed. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-18T16:49:20Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"yaml-validation",
"editors"
],
"locked": false,
"milestone": null,
"number": 1448,
"state": "closed",
"title": "Partial yaml completion regression",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1448"
} |
### Bug description
Quarto 1.0.28 is not finding a variable used in a caption. The error message is "object 'spe' not found". Here's a reproducible example:
---
title: "Test Report"
date: "`r Sys.Date()`"
toc: true
toc-depth: 4
format:
html:
code-tools: true
code-fold: true
code-link: false
---
# A Section
```{r}
spe <- 0.03
```
```{r}
#| label: fig-test
#| fig-cap: !expr paste('The lower left plot contains raw data (Spearman $\\rho=',spe[1],'$)')
plot(1:10)
```
I'm running Ubuntu 22.04
### `quarto check` Output
_No response_
### `quarto tools check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.28
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.4
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/harrelfe/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.11
[β] Checking Knitr engine render......OK
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-07-18T13:38:56Z",
"creator": "harrelfe",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1447,
"state": "open",
"title": "Quarto not finding a variable used in a capton",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1447"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1442
<div type='discussions-op-text'>
<sup>Originally posted by **msh855** July 18, 2022</sup>
Hi,
Is possible to include share buttons in each blog post so readers could share an article that I am writing in social media? (Linkedin, Twitter, Facebook etc.)
Thanks </div> | {
"assignee": "rich-iannone",
"comments": 1,
"created_at": "2022-07-18T13:37:24Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement",
"good-first-issue"
],
"locked": false,
"milestone": "v1.4",
"number": 1446,
"state": "open",
"title": "Ability to generate share buttons on blog posts",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1446"
} |
### Bug description
This relates to discussion in https://github.com/quarto-dev/quarto-cli/discussions/825 and comment in https://github.com/quarto-dev/quarto-cli/issues/1391#issuecomment-1186148935
When a custom footer is set to
````yaml
format:
revealjs:
footer: Custom footer
````
It is possible to hide it on a specific slide using the trick of inserting an empty slide footer
````
# Slide 2
content
::: footer
:::
````
However, this does not work on first slide at first
````markdown
---
format:
revealjs:
footer: Custom footer
---
# Slide 1
content
::: footer
:::
# Slide 2
content
````
This is because the feature (or free riding feature) rely on the per side footer overwrite using a `slidechanged` event which does not happen when presentation is loaded first time
https://github.com/quarto-dev/quarto-cli/blob/763b0ed7f060b206ef9b3a247612126b5f2f1f2a/src/resources/formats/revealjs/plugins/support/support.js#L117-L133
This means that in the example above if you go to slide 2 then back to slide 1, it will hide the footer.
Hiding footer on title slide can be useful when you want to do a custom one like in https://github.com/quarto-dev/quarto-cli/issues/1391#issuecomment-1186148935 example (https://github.com/giabaio/quarto-slides/blob/main/assets/title-slide.qmd)
Having a real mechanism to hide a footer (like adding `.no-footer` class on a slide maybe ?) would be a plus
| {
"assignee": null,
"comments": 2,
"created_at": "2022-07-18T09:20:57Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "Future",
"number": 1445,
"state": "open",
"title": "[FR] Ability to hide footer on specific slides including title-slide",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1445"
} |
### Bug description
Hi,
in [my yaml](https://github.com/ondata/consultazione-linee-guida-open-data/blob/main/_quarto.yml#L29=) I have
```
title: "#datiBeneComune per le Linee Guida Open Data"
```
In the rendered site instead I have
```
<meta name="twitter:title" content="#datiBeneComune per le Linee Guida Open Data - I commenti di #datiBeneComune alle Linee Guida Open Data">
```
This last is the title of the page, then the yaml config does not override it.
### `quarto check` Output
_No response_
### `quarto tools check` Output
```bash
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
```bash
[β] Checking Quarto installation......OK
Version: 1.0.28
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.2
Path: /usr/bin/python3
Jupyter: 4.10.0
Kernels: bash, python3, zsh
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.0.4
Path: /usr/lib/R
LibPaths:
- /home/aborruso/R/x86_64-pc-linux-gnu-library/4.0
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.13
[β] Checking Knitr engine render......OK
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-07-18T06:19:37Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1444,
"state": "closed",
"title": "twittercard override seems not work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1444"
} |
### Bug description
Code available at: https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli-1441
https://user-images.githubusercontent.com/8896044/179426952-4bebdf03-98a9-4fc8-b6e3-e115b4e59ab1.mov
I installed two formats via the extension mechanism (i.e., `quarto install extension umr1283/quarto-revealjs-umr1283`) which resulted in the following directory tree:
```default
.
βββ _extensions
β βββ dragonstyle
β β βββ lexcorp
β β βββ _extension.yml
β β βββ custom.scss
β β βββ logo.png
β β βββ title.png
β βββ umr1283
β βββ umr1283
β βββ _extension.yml
β βββ setup-ggplot2-umr1283.R
β βββ umr1283.scss
β βββ umr1283_8199.svg
βββ lexcorp.html
βββ lexcorp.qmd
βββ umr.html
βββ umr.qmd
```
But Quarto does not like the `_extensions/umr1283/umr1283` part.
```bash
quarto preview umr.qmd --no-browser --no-watch-inputs
WARNING: More than one extension is available for umr1283 in the directory /Users/mcanouil/Projects/misc/quarto-issues/quarto-cli-14xx/_extensions.
Extensions that match:
/Users/mcanouil/Projects/misc/quarto-issues/quarto-cli-14xx/_extensions/umr1283
/Users/mcanouil/Projects/misc/quarto-issues/quarto-cli-14xx/_extensions/umr1283/umr1283
ERROR: The extension 'umr1283' is missing the expected '_extensions.yml' file.
```
Changing the organisation name directory fix the issue, i.e., `_extensions/umr1283/umr1283` to `_extensions/umr1283-whatever/umr1283`.
I wonder if some kind of "lock" file (i.e., as for `renv`or `pak`) could be created at `_extensions` root, to get information about the installed extensions (e.g., commit SHA, tag, repo, etc.).
This could also help Quarto for different extensions sources such as subdirectory (#1440).
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.28
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.5
Path: /opt/homebrew/opt/[email protected]/bin/python3.10
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
(-) Checking R installation...........βΉ R version 4.2.1 (2022-06-23)
! Config '~/.Rprofile' was loaded!
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
``` | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-07-17T22:09:13Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 1441,
"state": "closed",
"title": "[Quarto Extension] Quarto does not like when org-name=extension-name",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1441"
} |
### Bug description
For stand alone Quarto documents, you can render them so that they have a title that evaluates an inline R chunk, i.e. this works:
```
---
title: "`r 1+1`"
format: html
---
## Quarto
```
and the title will be 2 (and also the pagetitle will be 2). This is expected behaviour.
However when this is a page in a website it no longer works. For example, if we have the following for our `_quarto.yml` file:
```
project:
type: website
website:
title: "Test"
```
Then the above page would have a title printed in the document of `2` but the pagetitle (title that appears in the browser tab) will be `Test - r 1+1` when it should really be `Test - 2`.
If I try to set the pagetitle directly, it still doesn't render properly, for example, the following Quarto document (when it's in the Quarto website) will have a tab name of `r 1+1`.
```
---
pagetitle: "`r 1+1`"
format: html
---
## Quarto
```
It's interesting that title works (in the document) but pagetitle does not seem to be working as expected.
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 99.9.9
Path: /Users/garthtarr/git/quarto-cli/package/dist/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.13
Path: /usr/local/opt/[email protected]/bin/python3.9
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/garthtarr/Library/R/x86_64/4.2/library
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Reading Tool Data
Tool Status Installed Latest
tinytex Not installed ---- v2022.07
chromium Not installed ---- 869685
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-07-17T14:15:45Z",
"creator": "garthtarr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1436,
"state": "open",
"title": "pagetitle not correctly rendering inline chunk evaluation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1436"
} |
While using RStudio, the following code can generate captions above the table.
```{r}
#| label: tbl-iris
#| tbl-cap: "Iris Data"
library(knitr)
kable(head(iris))
```
<img width="596" alt="Screen Shot 2022-07-03 at 13 00 46" src="https://user-images.githubusercontent.com/28393339/177034724-7bad2bc5-1325-4863-bcae-07e50e85b06e.png">
However, when I try the same code with **reactable** objects, it just ignores the caption.
```{r}
#| label: tbl-iris
#| tbl-cap: "Iris Data"
library(reactable)
reactable(head(iris))
```
<img width="614" alt="Screen Shot 2022-07-03 at 13 00 01" src="https://user-images.githubusercontent.com/28393339/177034705-0409abe2-d0db-497d-bd05-631fb5f29e25.png">
How can I solve the problem?
| {
"assignee": null,
"comments": 1,
"created_at": "2022-07-17T11:46:06Z",
"creator": "canholyavkin",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1435,
"state": "closed",
"title": "Unable to add captions to reactable objects ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1435"
} |
I'll often need to output documents using a [Word template](https://quarto.org/docs/output-formats/ms-word-templates.html) (where the ultimate target is actually Google Docs instead of Microsoft word).
With my limited design skills, I've messed around with the default template a bit in the past with mixed results.
I think there would be value in establishing a centralized repo or gallery for community-created templates, and it would probably get more traction if it was "official" in some sense, perhaps linked to the documentation here: https://quarto.org/docs/output-formats/ms-word-templates.html
Thoughts? | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-16T21:02:35Z",
"creator": "ajfriend",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1432,
"state": "open",
"title": "Establish a Word template gallery?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1432"
} |
### Bug description
If you include a citation in a `revealjs` presentation, the link for the citation should go to the last slide with references instead of the first slide.
Here is a slide:
```` markdown
---
format: revealjs
bibliography: references.bib
---
## Slide 1
Slide 1 text.
## Slide 2
Slide 2 text.
[@gorman2014]
## References
````
And here is the contents of `references.bib`:
``` markdown
@article{gorman2014,
title = {Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis)},
author = {Gorman, Kristen B. and Williams, Tony D. and Fraser, William R.},
year = {2014},
month = {03},
date = {2014-03-05},
journal = {PLOS ONE},
pages = {e90081},
volume = {9},
number = {3},
doi = {10.1371/journal.pone.0090081},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0090081},
note = {Publisher: Public Library of Science},
langid = {en}
}
```
Inspecting the link on Slide 2:
``` html
<a href="#/ref-gorman2014" role="doc-biblioref" onclick="return false;" aria-expanded="false">Gorman, Williams, and Fraser 2014</a>
```
`#/ref-gorman2014` goes to Slide 1 instead of last slide. Either disabling the clickable link or pointing it to the last slide would resolve the issue.
- Quarto version: 1.0.28
- RStudio version: RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_4_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
- OS: macOS 12.4
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-07-16T19:26:54Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1431,
"state": "closed",
"title": "References links in revealjs presentation goes to first slide, should go to last",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1431"
} |
### Bug description
When rendering a qmd file with VSCode extension, i.e., using the "render" button, the UTF-8 characters are not rendered properly when knitr engine is used.
<details><summary>See quarto code</summary>
````
---
title: "Untitled"
format: gfm
---
```{r}
1
```
Des accents: éèΓͺà çôâ
````
</details>
<img width="600" alt="image" src="https://user-images.githubusercontent.com/8896044/179362288-7f30bcb8-4ca2-4955-bb26-a5d36820b942.png">
Without the R cell chunk, the rendered document is just fine.
<details><summary>See quarto code</summary>
````
---
title: "Untitled"
format: gfm
---
Des accents: éèΓͺà çôâ
````
</details>
<img width="600" alt="image" src="https://user-images.githubusercontent.com/8896044/179362304-59aed159-7cfe-4e26-9677-27084bf0ec25.png">
There is no problem using quarto cli (or using quarto R package):
<img width="350" alt="image" src="https://user-images.githubusercontent.com/8896044/179362412-4a2a9251-89ef-4b95-9cb2-d0af9d45bdad.png"><img width="350" alt="image" src="https://user-images.githubusercontent.com/8896044/179362384-e678266e-8430-4306-9637-689827d35e44.png">
Code: https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli-1429
OS: MacOS latest (arm64)
R: 4.2.1
Quarto: 1.0.25
VSCode/Extension: latest
<details><summary>See `.Rprofile` content</summary>
```
if (nzchar(system.file(package = "cli"))) {
cli::cli_alert_info(R.version.string)
cli::cli_alert_warning(paste0("Config '", cli::col_green("~/.Rprofile"), "' was loaded!"))
} else {
message(R.version.string)
message("Config '~/.Rprofile' was loaded!")
}
options(
languageserver.formatting_style = function(options, ...) {
transformers <- styler::tidyverse_style(indent_by = options$tabSize, ...)
transformers$indention$update_indention_ref_fun_dec <- NULL
transformers$indention$unindent_fun_dec <- NULL
transformers$line_break$remove_line_breaks_in_fun_dec <- NULL
transformers
}
)
if (interactive()) {
options(
repos = c(
"CRAN" = if (is.null(getOption("repos")[["CRAN"]]) || getOption("repos")[["CRAN"]] %in% "@CRAN@") {
"https://cran.r-project.org/"
} else {
getOption("repos")[["CRAN"]]
}
),
width = 150,
menu.graphics = FALSE,
reprex.advertise = FALSE,
usethis.protocol = "https",
usethis.full_name = "MickaΓ«l Canouil",
usethis.description = list(
`Authors@R` = paste0(
"person(",
'given = "MickaΓ«l", ',
'family = "Canouil", ',
'role = c("aut", "cre"), ',
'email = "[email protected]", ',
'comment = c(ORCID = "0000-0002-3396-454")',
")"
),
Version = "0.0.0.9000"
)
)
if (nzchar(system.file(package = "devtools"))) library(devtools, quietly = TRUE, warn.conflicts = FALSE)
if (nzchar(system.file(package = "prompt"))) prompt::set_prompt(prompt::prompt_git)
}
```
</details>
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.25
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.5
Path: /opt/homebrew/opt/[email protected]/bin/python3.10
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
(-) Checking R installation...........βΉ R version 4.2.1 (2022-06-23)
! Config '~/.Rprofile' was loaded!
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
| {
"assignee": null,
"comments": 2,
"created_at": "2022-07-16T16:02:34Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1429,
"state": "closed",
"title": "UTF-8 characters not properly rendered via VSCode \"render\" button",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1429"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1413
<div type='discussions-op-text'>
<sup>Originally posted by **jmgirard** July 15, 2022</sup>
The line numbers in a code block are automatically linked to `#cb1-1`, `#cb1-2`, etc. But these don't really work in the context of a RevealJS Presentation. Clicking the links just brings you back to the first/title slide. Can we get the option to disable code line number links?
---
title: "Untitled"
format: revealjs
---
```{r}
#| echo: true
#| eval: false
1
2
3
```
</div> | {
"assignee": "cderv",
"comments": 1,
"created_at": "2022-07-16T14:27:45Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1427,
"state": "open",
"title": "Code Line Number Links in RevealJS Presentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1427"
} |
### Bug description
@mine-cetinkaya-rundel observed a case where an older terminal session within RStudio had a `TMPDIR` value that had been cleaned up by the system. This makes it impossible for Quarto CLI to start as the call to `Deno.makeTempDirSync()` fails. We should find a way to gracefully recover and choose another valid `TMPDIR` location.
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-07-16T13:27:34Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1425,
"state": "closed",
"title": "Recover from missing TMPDIR in Deno.makeTempDirSync",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1425"
} |
### Bug description
The theme toggle icon isn't centred, it would be good to make it centred so it stays in line with the other icons. For reference, here's what the icon looks like:
<img width="245" alt="Screenshot 2022-07-16 at 10 21 39" src="https://user-images.githubusercontent.com/3131401/179347562-c45cdb7e-9d4b-4344-82ab-2af3bd0d20b8.png">
Here's the proposed change:
<img width="161" alt="Screenshot 2022-07-16 at 10 24 25" src="https://user-images.githubusercontent.com/3131401/179347573-82610d76-9bed-46f4-9926-9077d24d021b.png">
Here's a reproducible `_quatro.yml`:
```yaml
book:
title: "Test"
navbar:
background: primary
search: true
```
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.27
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.7 (Conda)
Path: /Users/fabiorosado/miniconda3/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-07-16T08:45:10Z",
"creator": "FabioRosado",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1422,
"state": "closed",
"title": "Theme toggle isn't centred in navbar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1422"
} |
I have created a post with images read from my local machine, but in the preview, the images do not show up:
I just use markdown to create the post. In my markdown app, images show up perfectly. Here is the code:
`
` | {
"assignee": null,
"comments": 3,
"created_at": "2022-07-16T07:51:43Z",
"creator": "ghost",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1421,
"state": "closed",
"title": "Images does not show up",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1421"
} |
### Bug description
I'm running CentOS 7 so the version of deno that's packaged with the current Quarto-CLI is incompatible with my system (see https://github.com/denoland/deno/issues/1658).
The workaround was to install deno using conda:
`mamba install -c conda-forge deno`
After that I copied this CentOS7-compatible binary to the original location in the Quarto-CLI folder.
I first did this after installing Quarto CLI from https://github.com/quarto-dev/quarto-cli/releases/download/v1.0.28/quarto-1.0.28-linux-amd64.tar.gz. I ran the following command and got the subsequent error:
```
$ ~/software/quarto-1.0.28/bin/quarto tools check
error: Found argument '--no-config' which wasn't expected, or isn't valid in this context
USAGE:
deno run <SCRIPT_ARG>... --unstable
For more information try --help
```
I installed Quarto 1.0.18 instead, which precedes this [pull request](https://github.com/quarto-dev/quarto-cli/pull/1388).
```
$ ~/software/quarto-1.0.18/bin/quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
Details about my deno install:
```
$ ~/software/quarto-1.0.18/bin/tools/deno --version
deno 1.17.0 (release, x86_64-unknown-linux-gnu)
v8 9.7.106.15
typescript 4.5.2
```
Reporting this bug in case others trying to run Quarto on CentOS 7 have similar issues implementing this workaround.
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-07-16T03:40:27Z",
"creator": "lkhilton",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1420,
"state": "closed",
"title": "New `--no-config` argument is incompatible with some versions of deno",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1420"
} |
Observable JS doesn't seem to work without network connectivity because dependencies are pulled in at runtime (e.g., `htl`).
Haven't explored this in depth, but it seems that for recommended libraries like Inputs, I can download a local copy and require from an OJS chunk (since these get inlined?). But this doesn't work with `htl`, which might be needed earlier by the runtime. If this is complicated, perhaps there could be an option to include a "heavyweight" stdlib with all dependencies bundled (regardless of whether they're used or not) in the short-term?
More generally, it'd be nice if all JS/Observable dependencies were inlined for a self-contained document, rather than just the local ones... it seems this can be worked around by fetching local copies, but it's a bit cumbersome, and automating it behind the scenes would make code a little more immediately portable between QbservableHQ and Quarto.
I'm running Quarto 1.0.23.
Thanks so much for the awesome work and creating this amazing tool! | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-07-15T17:45:01Z",
"creator": "arbelt",
"is_pull_request": false,
"labels": [
"enhancement",
"ojs-engine"
],
"locked": false,
"milestone": "Future",
"number": 1412,
"state": "open",
"title": "Documents using Observable JS are not self-contained",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1412"
} |
### Bug description
In my documents, I prefer to write each new sentence in a new line so changes are easier to track on GitHub. However, Quarto deletes line breaks and merges separate sentences into a single line if I switch between source and visual view.
It is hard to generate a reproducible example because the issue only arises when switching between views, so here is a `.gif` of what it looks like.
Here is the corresponding code (before the linebreaks get deleted):
```R
---
title: "Linebreak Test"
format: html
editor: visual
---
## Heading
This is my first sentence.
This is my second sentence.
Here is another sentence.
```
The problem occurs in R versions 4.2.0 and 4.2.1, RStudio version 2022.2.3.492 and 2022.7.0.548 on Windows 11 (Version 21H2 (OS Build 22000.795).
Result of `xfun::session_info('rmarkdown')`:
```
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000), RStudio 2022.7.0.548
Locale:
LC_COLLATE=English_Germany.utf8
LC_CTYPE=English_Germany.utf8
LC_MONETARY=English_Germany.utf8
LC_NUMERIC=C
LC_TIME=English_Germany.utf8
Package version:
base64enc_0.1.3 bslib_0.3.1 digest_0.6.29 evaluate_0.15
fastmap_1.1.0 fs_1.5.2 glue_1.6.2 graphics_4.2.1
grDevices_4.2.1 highr_0.9 htmltools_0.5.2 jquerylib_0.1.4
jsonlite_1.8.0 knitr_1.39 magrittr_2.0.3 methods_4.2.1
R6_2.5.1 rappdirs_0.3.3 rlang_1.0.4 rmarkdown_2.14
sass_0.4.1 stats_4.2.1 stringi_1.7.8 stringr_1.4.0
tinytex_0.40 tools_4.2.1 utils_4.2.1 xfun_0.31
yaml_2.3.5
Pandoc version: 2.18
```
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.18
Path: C:\Program Files\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.7 (Conda)
Path: C:/ProgramData/Anaconda3/python.exe
Jupyter: 4.8.1
Kernels: python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.2.1
Path: C:/PROGRA~1/R/R-42~1.1
LibPaths:
- C:/Program Files/R/R-4.2.1/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 4,
"created_at": "2022-07-15T14:27:09Z",
"creator": "einGlasRotwein",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1409,
"state": "closed",
"title": "Line breaks get deleted when moving between source and visual",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1409"
} |
### Bug description
* Open a new quarto document from RStudio IDE
* Try adding some chunk option like `eval` , `include`, `echo` using autocomplete after `#|` - the options are not suggested anymore.
There my be other but that is the one found by user (reported on internal slack)
Using last dev version of Quarto in last daily version of IDE | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-07-15T12:21:41Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1407,
"state": "closed",
"title": "Autocomplete is broken for some chunk options",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1407"
} |
### Bug description
Can't retrieve author name using meta shortcode `{{< meta author >}}` as discussed in https://github.com/quarto-dev/quarto-cli/issues/1391#issuecomment-1185384785
````
---
title: "My title"
author: "MickaΓ«l Canouil"
date: last-modified
format: html
self-contained: true
---
{{< meta title >}}
{{< meta author >}}
{{< meta author.name >}}
{{< meta date >}}
````
<img width="1624" alt="image" src="https://user-images.githubusercontent.com/8896044/179202138-a9ffc243-1d5f-4b33-9cc6-e244735ee217.png">
Code: https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli-1406
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.20
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.5
Path: /opt/homebrew/opt/[email protected]/bin/python3.10
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
(-) Checking R installation...........βΉ R version 4.2.1 (2022-06-23)
! Config '~/.Rprofile' was loaded!
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
``` | {
"assignee": null,
"comments": 5,
"created_at": "2022-07-15T10:07:23Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1406,
"state": "closed",
"title": "Can't retrieve author name using meta shortcode `{{< meta author >}}`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1406"
} |
### Bug description
When authoring slides in revealjs format, the following slide, featuring nested spans, renders as intended: each fragment fading in on click, each with a colored span, all in the same paragraph.
```markdown
---
format: revealjs
---
## Title
::: {style="text-align: center"}
[One [hen]{style="color: red"}]{.fragment} [two [ducks]{style="color: blue"}]{.fragment}
:::
```
When I click into the visual editor, then click back, the sourced has been changed to:
```markdown
---
format: revealjs
---
## Title
::: {style="text-align: center"}
[One ]{.fragment}[hen]{style="color: red"} [two ]{.fragment}[ducks]{style="color: blue"}
:::
```
In other words, it unnests the spans, which has the effect of breaking the animation.
I can fix the animation by putting the fade in fragments as divs instead of spans, but then it breaks the all-in-one-paragraph layout.
This is using the RStudio IDE 2022.07.0 Build 548 "Spotted Wakerobin" on MacOS Catalina 10.15.7.
Thanks for the help!
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.20
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.1
Path: /usr/local/bin/python3
Jupyter: 4.11.0
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
``` | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-14T22:35:34Z",
"creator": "andrewpbray",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1403,
"state": "open",
"title": "Visual editor reformats nested spans",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1403"
} |
### Bug description
Pages like https://quarto.org/docs/guide/ have a sidebar with sections of content. I'm looking to recreate that kind of sidebar, but with text headings for each section, similar to R for Data Science:
It looks like if you add a content item to the sidebar that's just text (e.g. "Some header"), then it doesn't appear:
```
sidebar:
- id: get-started
# ...
contents:
- text: "Some header"
```
However, if you add a horizontal rule, then it shows up in the sidebar:
```
sidebar:
- id: get-started
# ...
contents:
- text: "----------------"
```
### `quarto check` Output
Note that this is on Mac OSX
```bash
[β] Checking Quarto installation......OK
Version: 1.0.20
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.2
Path: /Users/machow/.virtualenvs/pyshiny-site/bin/python3
Jupyter: 4.10.0
Kernels: venv-siuba, venv-pins-python, venv-vetiver-test, venv-intro-to-siuba, venv-vetiver-python, venv-shiny-examples, venv-pyshiny-site, venv-notes, venv-siuba-docs, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.1.2
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 10,
"created_at": "2022-07-14T19:31:15Z",
"creator": "machow",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1400,
"state": "closed",
"title": "website unable to put plain text entry into sidebar, like R4DS",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1400"
} |
I am using Quarto in VSCode. I wonder whether it is possible to use the autocomplete facilities for cross-references and citations. This is a convenient functionality, but I could not find it anywhere. | {
"assignee": null,
"comments": 4,
"created_at": "2022-07-14T19:22:55Z",
"creator": "VivaldoMendes",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1399,
"state": "open",
"title": "Autocomplete: Quarto for VSCode",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1399"
} |
I am trying to follow the [render targets](https://quarto.org/docs/websites/#render-targets) instructions for ignoring a folder in a Quarto website, but it seems Quarto is still rendering everything in that folder. Here's my example:
After creating a demo website with `quarto create-project mysite --type website`, I edit the `_quarto.yml` file as follows:
```
project:
type: website
output-dir: _site
render:
- "*.qmd"
- "!dontrender/"
website:
title: "quarto-blog"
navbar:
right:
- about.qmd
- icon: github
href: https://github.com/
- icon: twitter
href: https://twitter.com
format:
html:
theme: cosmo
css: styles.css
```
I then created a folder called `dontrender` and inserted a `test.qmd` containing the following:
```
---
title: "test"
---
```
When I use `quarto render`, the `test.qmd` file still gets rendered despite my `"!dontrender/"` command in the `_quarto.yml` file. | {
"assignee": null,
"comments": 4,
"created_at": "2022-07-14T16:09:00Z",
"creator": "jhelvy",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1394,
"state": "closed",
"title": "`quarto render` still rendering ignored folders",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1394"
} |
Discuss how to best deal with replacing this command (e.g. make a new general command for getting machine readable status vs adding flag to `quarto check` to support machine readable output). | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-07-14T14:25:57Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 1393,
"state": "open",
"title": "Replace `quarto tools info <toolname>`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1393"
} |
Print tools info for users as a part of `quarto check` (print pretty human readable form).
Remove `quarto tools info` from bug template | {
"assignee": "dragonstyle",
"comments": 8,
"created_at": "2022-07-14T14:22:45Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement",
"good-first-issue",
"quarto-check"
],
"locked": false,
"milestone": "v1.4",
"number": 1392,
"state": "open",
"title": "Add Tools Info to `quarto check`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1392"
} |
I may be missing something obvious, but I would like to do that. I'm working on a quarto slide presentation (formatted in revealjs) and I have defined a bunch of objects in the `params` variable in my YAML
```
---
...
params:
title: "My title"
author: Gianluca Baio
date: 27 November 2022
institute: "[My work](Their website)"
conference: "Where I'm speaking"
location: "What town"
...
---
HERE GOES THE REST OF MY SLIDES
```
What I would like to do is to use the elements of `params` to feed to the `footer` that I want to use for the slides, something like
```
...
format:
revealjs:
footer: `r params$author` | `r params$title` | `r params$date`
```
but it seems like I can't use the
```
`r command`
```
tag inside the yaml, as it returns an error
```
bad indentation of a mapping entry at line 9, column 10:
footer: `r params$author`
```
Like I said, it's possible I am not doing this right --- but can anyone explain why and how I can do it instead?
Thanks
Gianluca | {
"assignee": null,
"comments": 30,
"created_at": "2022-07-14T12:26:48Z",
"creator": "giabaio",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1391,
"state": "open",
"title": "Can I use R variables in quarto YAML?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1391"
} |
If you run quarto from a directory that has a deno.jsonc file, deno thinks that this file is there to configure itself, and it honors that file. So if that file changes compiles flags incompatibly, quarto just fails.
The fix appears to be to add `--no-config` to QUARTO_DENO_OPTIONS.
| {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-14T00:38:41Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1387,
"state": "closed",
"title": "quarto needs to ignore `deno.jsonc`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1387"
} |
### Bug description
1. Create a new Quarto project using the RStudio IDE. Let's call it `~/Desktop/qp`.
This project needs to be within a directory that RStudio can access, but is not allowed to the Terminal.app. On my laptop, the `~/Desktop` directory fits this criteria. The Security&Privacy / Privacy / Files and Folders preferences can be adjusted so RStudio can create a project beneath the Desktop without allowing Terminal access.
2. Start the Terminal.app. Change directory into the `~/Desktop/qp` directory. If the system asks for desktop access, do not allow it.
```bash
cd ~/Desktop/qp
```
Interestingly, the `cd` command succeeds even though things like `ls` fail.
3. Attempt any Quarto operation within this restricted directory:
```bash
quarto render index.qmd
```
The resulting output:
```default
============================================================
Deno has panicked. This is a bug in Deno. Please report this
at https://github.com/denoland/deno/issues/new.
If you can reliably reproduce this panic, include the
reproduction steps and re-run with the RUST_BACKTRACE=1 env
var set and include the backtrace in your report.
Platform: macos x86_64
Version: 1.22.0
Args: ["/Users/aron/dev/rstudio/quarto-cli/package/dist/bin/tools/deno", "run", "--unstable", "--cached-only", "--allow-read", "--allow-write", "--allow-run", "--allow-env", "--allow-net", "--allow-ffi", "--importmap=/Users/aron/dev/rstudio/quarto-cli/src/dev_import_map.json", "/Users/aron/dev/rstudio/quarto-cli/src/quarto.ts", "render", "index.qmd"]
thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: Os { code: 1, kind: PermissionDenied, message: "Operation not permitted" }', core/module_specifier.rs:141:28
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
```
### `quarto check` Output
The `quarto check` command did not succeed within the restricted directory. It erred with the same output as above.
When run from a different directory:
```default
[β] Checking Quarto installation......OK
Version: 99.9.9
Path: /Users/aron/dev/rstudio/quarto-cli/package/dist/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.9
Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 3.6.3
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/aron/Library/R/3.6/library
- /Library/Frameworks/R.framework/Versions/3.6/Resources/library
rmarkdown: 2.11.16
[β] Checking Knitr engine render......OK
```
This issue was confirmed while using commit 852a0231c043417a0f848faed90af1116a2c8fb4. It occurs in earlier versions, as well.
Tested on macOS Monterey - 12.4
Quarto website project was created using RStudio 2022.07.0 Build 548
### `quarto tools check` Output
The `quarto tools check` command did not succeed within the restricted directory. It erred with the same output as above.
When run from a different directory:
```default
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included 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] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 0,
"created_at": "2022-07-13T17:03:52Z",
"creator": "aronatkins",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1379,
"state": "open",
"title": "Deno panic when directory access not permitted",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1379"
} |
### Bug description
This is a minimal reprex after digging into the issue reported in https://github.com/quarto-dev/quarto-cli/issues/1108#issuecomment-1182964857 where discussion happened in https://github.com/mpadge/quarto-test/issues/1
This is a special case from converting some Bookdown project to Quarto Book, but I believe this is really an issue in Quarto at the end.
TL;DR;: HTML dependencies returned in `knit_meta` are included in the header when converting to PDF which obviously leads to a LaTeX error.
See this simple example
````
---
always_allow_html: true
---
```{r}
htmltools::tagList(rmarkdown::html_dependency_font_awesome())
htmltools::div(class="dummy",
htmltools::p("HTML content"))
```
````
By inserting `always_allow_html: true`, it means that even when converting to PDF the code chunk will be evaluated.
Without it we get an error thrown by **rmarkdown**
````
Error:
! Functions that produce HTML output found in document targeting pdf output.
Please change the output type of this document to HTML. Alternatively, you can allow
HTML output in non-HTML formats by adding this option to the YAML front-matter of
your rmarkdown file:
always_allow_html: true
Note however that the HTML output will not be visible in non-HTML formats.
````
By allowing `always_allow_html: true`, the content will be included in the md file within raw HTML block, which we get also in Quarto
````
::: {.cell-output-display}
```{=html}
<div class="dummy">
<p>HTML content</p>
</div>
```
:::
````
This will insure the output is not included in PDF output.
However, Quarto does not filter the HTML dependencies part as it is done in `rmarkdown::pdf_document()` by `has_latex_dependencies(knit_meta)`
https://github.com/rstudio/rmarkdown/blob/d23e479017ceec894cc62c6b98f40f4188a4a75f/R/pdf_document.R#L177-L81
This means that the `.tex` file in Quarto will contain this
````tex
\makeatother
<link href="test2_files/libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="test2_files/libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
\KOMAoption{captions}{tableheading}
````
HTML dependencies are resolved like HTML and inserted in the header part of the template.
We should probably fix this.
### `quarto check` Output
````bash
quarto check
[>] Checking Quarto installation......OK
Version: 99.9.9
Path: C:\Users\chris\Documents\DEV_R\quarto-cli\package\dist\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.12
Path: C:/Users/chris/scoop/apps/pyenv/current/pyenv-win/versions/3.9.12/python.exe
Jupyter: 4.10.0
Kernels: bash, julia-1.7, python3
[>] Checking Jupyter engine render....OK
(\) Checking R installation...........++ Activating rlang global_entrace
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/PROGRA~1/R/R-42~1.0
LibPaths:
- C:/Users/chris/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.0/library
rmarkdown: 2.14.3
[>] Checking Knitr engine render......OK
````
### `quarto tools check` Output
````bash
quarto tools check
[>] Inspecting tools
Tool Status Installed Latest
chromium Up to date 869685 869685
tinytex External Installation --- v2022.07
````
Rstudio IDE 2022.10.0-daily+64 on Windows 11
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-07-13T16:50:12Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1378,
"state": "closed",
"title": "HTML dependencies are not filtered out from being included in PDF output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1378"
} |
### Bug description
Hello,
The output-location feature is not working for me while making quarto slides in Rstudio. Below is a reproducible example with screenshot. none of the options of the feature are working (fragment, column, slide). The output continues to show up below the code on the same slide.
Rstudio version 2022.02.3 Build 492
macOS Monterey version 12.3.1(21E258)
Quarto Version: 0.9.80
````
---
title: "test"
format: revealjs
---
## Executable Code
```{r}
#| echo: true
#| output-location: slide
3+4
```
````
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 0.9.80
Path: /Applications/RStudio.app/Contents/MacOS/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.7.4
Path: /usr/local/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
meenakshikushwaha@MacBook-Pro 2022_July_quarto-slides_data-wrangling % Checking R installation...........OK
quarto tools check
zsh: command not found: Checking
[β] Reading Tool Data
Tool Status Installed Latest
tinytex Present - ext. managed ---- v2022.07
meenakshikushwaha@MacBook-Pro 2022_July_quarto-slides_data-wrangling % /usr/local/bin/quarto check
zsh: no such file or directory: /usr/local/bin/quarto
meenakshikushwaha@MacBook-Pro 2022_July_quarto-slides_data-wrangling % quarto check
[β] Checking Quarto installation......OK
Version: 0.9.80
Path: /Applications/RStudio.app/Contents/MacOS/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.7.4
Path: /usr/local/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
### `quarto tools check` Output
<img width="550" alt="image" src="https://user-images.githubusercontent.com/52627451/178777342-186797da-6874-4392-8c6d-a1ea11d85d4f.png">
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 6,
"created_at": "2022-07-13T16:19:48Z",
"creator": "meenakshi-kushwaha",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1377,
"state": "closed",
"title": "output-location not working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1377"
} |
{
"assignee": null,
"comments": 2,
"created_at": "2022-07-13T12:51:39Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1374,
"state": "closed",
"title": "documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the \"Quarto Tools Check Output\" text area?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1374"
} |
|
### Bug description
Here is a simple qmd file:
````
---
title: "Hello"
format:
html:
code-tools:
source: https://github.com/quarto-dev/quarto-web/blob/main/index.md
---
Some text.
```{r}
1 + 1
```
````
When rendered, the `code-tools` menu doesn't show up.
<img width="1552" alt="Screen Shot 2022-07-12 at 8 15 20 PM" src="https://user-images.githubusercontent.com/5965649/178663604-53528fea-7e3d-4d21-bedb-20cea6998618.png">
Things work fine if using `source: true`.
<img width="1552" alt="Screen Shot 2022-07-12 at 8 16 13 PM" src="https://user-images.githubusercontent.com/5965649/178663783-271ec5a1-8f2d-4fb8-8289-29c9942ecdea.png">
- RStudio version: RStudio 2022.07.0+548 "Spotted Wakerobin" Release (34ea3031089fa4e38738a9256d6fa6d70629c822, 2022-07-06) for macOS Mozilla/5.0 (Macintosh; Intel Mac OS X 12_4_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
- OS: macOS 12.4
### `quarto check` Output
``` bash
[β] Checking Quarto installation......OK
Version: 1.0.16
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.1
Path: /usr/local/bin/python3
Jupyter: 4.9.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/mine/Desktop/RStudio/quarto-tip-a-day/renv/library/R-4.2/x86_64-apple-darwin17.0
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
``` bash
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-13T06:19:10Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1371,
"state": "closed",
"title": "`code-tools` doesn't work with URL for `source`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1371"
} |
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