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### Bug description
Adding the following to the YAML of the template Quarto Document results in source code that is too light to be legible.
``` yaml
format:
html:
code-tools: true
highlight-style: a11y-dark
```
<img width="1552" alt="Screen Shot 2022-07-12 at 6 59 10 PM" src="https://user-images.githubusercontent.com/5965649/178654546-99f28b1b-f9b9-4ee2-b97d-c59f81e652f7.png">
- Quarto version: 1.0.16
- OS: macOS 12.4
- 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
### `quarto check` Output
```
[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
```
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] #1374
- [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": "2022-07-13T05:06:22Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1370,
"state": "closed",
"title": "Highlighting code-tools source code not legible with highlight-style: a11y-dark ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1370"
} |
I set up the Julia kernel for Quarto documents in RStudio, following the instructions on the Quarto website, and I reproduced the Plots demo in <https://quarto.org/docs/computations/julia.html>
However, when I installed the Julia package **Luxor**, I rendered my Quarto document without any errors, but it did not produce a plot of the turtle graphics (only the value `true`) that I was trying to reproduce from <https://juliagraphics.github.io/Luxor.jl/v1.0/turtle.html>
I did modify the Julia code in their example and removed the turtle emoji and the turtle image (turtles.png). I thought that maybe the issue was related to the graphics device and tried using different graphics devices, but to no avail.
It appears that the drawing function can create a file with the drawing, which can be specified in the function `Drawing(600, 400, :png, "test.png")` with the file name `test.png`, but also have the png file in the memory, specified by the argument `:png`. So, I just loaded the image file after the Julia code gets executed. I guess that's one quick solution, but it would be much better if the graphics get captured and properly embedded into the final output after rendering the qmd document. I also wondered how to suppress the value `true` being returned when I render the qmd document. The chunk option `results='hide'` does not to work.
> Finally, when I run the Julia code chunk inside the Quarto document, RStudio crashes, the R session gets aborted and I have to restart my R session. I do have the **JuliaCall** R package installed. Below is the qmd file, where the Julia packages **Luxor** and **Colors** have been installed:
````
---
title: "Luxor Turtle Graphics"
format: html
---
```{julia}
using Luxor, Colors
Drawing(600, 400, :png, "test.png")
origin()
background("midnightblue")
t = Turtle()
Pencolor(t, "cyan")
Penwidth(t, 1.5)
global n = 5
for i in 1:400
Forward(t, n)
Turn(t, 89.5)
HueShift(t)
n += 0.75
end
fontsize(20)
finish()
```
{width="70%"}
````
| {
"assignee": null,
"comments": 0,
"created_at": "2022-07-13T04:19:17Z",
"creator": "bkostadi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1369,
"state": "open",
"title": "Vector graphics produced by the Julia Luxor package not being rendered in Quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1369"
} |
### Bug description
Here is the type of output that I get if I activate logging from Pandoc
````
quarto render --verbose
[1/2] about.qmd
[INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\template.patched from C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\template.patched
[INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\metadata.html from C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\metadata.html
[INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\title-block.html from C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\title-block.html
[INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\title-metadata.html from C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\title-metadata.html
[INFO] Loaded C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\toc.html from C:\Users\chris\AppData\Local\Temp\quarto-sessioneaff13ab\68446796\860cba26\toc.html
[INFO] Running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/quarto-init/quarto-init.lua
[INFO] Completed filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/quarto-init/quarto-init.lua in 0 ms
[INFO] Running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/authors/authors.lua
[INFO] Completed filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/authors/authors.lua in 15 ms
[INFO] Running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/quarto-pre/quarto-pre.lua
[INFO] Completed filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/quarto-pre/quarto-pre.lua in 31 ms
[INFO] Running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/crossref/crossref.lua
[INFO] Completed filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/crossref/crossref.lua in 15 ms
[INFO] Running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/layout/layout.lua
[INFO] Completed filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/layout/layout.lua in 15 ms
[INFO] Running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/quarto-post/quarto-post.lua
[INFO] Completed filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/quarto-post/quarto-post.lua in 0 ms
[INFO] Running filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/quarto-finalize/quarto-finalize.lua
[INFO] Completed filter C:/Users/chris/Documents/DEV_R/quarto-cli/src/resources/filters/quarto-finalize/quarto-finalize.lua in 15 ms
[INFO] Not rendering RawInline (Format "tex") "\\Users"
[INFO] Not rendering RawInline (Format "tex") "\\chris"
[INFO] Not rendering RawInline (Format "tex") "\\Documents"
[INFO] Not rendering RawInline (Format "tex") "\\DEV"
[INFO] Not rendering RawInline (Format "tex") "\\quarto"
[INFO] Not rendering RawInline (Format "tex") "\\src"
[INFO] Not rendering RawInline (Format "tex") "\\resources"
[INFO] Not rendering RawInline (Format "tex") "\\formats"
[INFO] Not rendering RawInline (Format "tex") "\\html"
[INFO] Not rendering RawInline (Format "tex") "\\templates"
[INFO] Not rendering RawInline (Format "tex") "\\Users"
[INFO] Not rendering RawInline (Format "tex") "\\chris"
[INFO] Not rendering RawInline (Format "tex") "\\Documents"
[INFO] Not rendering RawInline (Format "tex") "\\DEV"
[INFO] Not rendering RawInline (Format "tex") "\\quarto"
[INFO] Not rendering RawInline (Format "tex") "\\src"
[INFO] Not rendering RawInline (Format "tex") "\\resources"
[INFO] Not rendering RawInline (Format "tex") "\\formats"
[INFO] Not rendering RawInline (Format "tex") "\\html"
[INFO] Not rendering RawInline (Format "tex") "\\templates"
````
the last part shows something is off with parsing a file path
After looking into this with @dragonstyle , this comes from the content of the metadata file we are building and passing to Pandoc
Part of the content is
````yaml
template-partials:
- 'C:\Users\chris\Documents\DEV_R\quarto-cli\src\resources\formats\html\templates\title-block.html'
- 'C:\Users\chris\Documents\DEV_R\quarto-cli\src\resources\formats\html\templates\title-metadata.html'
````
Metadata file in YAML has its string values parsed as Markdown (https://pandoc.org/MANUAL.html#option--metadata-file) and this is failling to parse the `template-partials` values because `\` is not escaped as it should in Markdown, so it is seen by Pandoc and rawInline with format tex.
Probably this fields should either:
* Use double backslash or forward slash
* Be removed from the metatafile passed to Pandoc command as they are probably not necessing at rendering time by Pandoc. (only used by Quarto in preprocessing step ?)
Anyway, it is causing no specific issue here, but should be fixed at some point.
### `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": null,
"comments": 1,
"created_at": "2022-07-12T21:10:41Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1367,
"state": "closed",
"title": "`template-partials` metadata cause parsing failure logged in Pandoc ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1367"
} |
### Bug description
I've been playing on the **RStudio Cloud** with the **matplotlib demo** from the Quarto documentation on **Using Python** - <https://quarto.org/docs/computations/python.html>. I followed the instructions and I installed **jupyter** and **matplotlib**, python 3.8 and numpy are already installed. I rendered the matplotlib demo qmd successfully, however when I tried running the python chunk inside the qmd, I was prompted to update **jsonlite** and **reticulate**, then I got the errors:
- `there is no package called 'reticulate'`,
- `No non-system installation of Python could be found. Would you like to download and install Miniconda?`
I said `yes` to installing **miniconda**, but then I got the error message `Error creating conda environment 'r-reticulate' [exit code 137]`. Despite this error, a new python environment must have been created because I was able to run a python chunk with basic math computations with `import math`, but I still could not run the chunk based on **matplotlib** since now a different python environment was being used rather than the jupyter python kernel where I had installed **matplotlib**.
Finally, I tried to render the qmd file again, but now the rendering failed with the error message:
```
Starting Jupyter kernel.../home/r157428/.local/lib/python3.8/site-packages/jupyter_client/__init__.py:23: UserWarning: Could not import submodules
warnings.warn("Could not import submodules")
Traceback (most recent call last):
File "/opt/quarto/0.9.293/share/jupyter/jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "/opt/quarto/0.9.293/share/jupyter/notebook.py", line 14, in <module>
from nbclient import NotebookClient
File "/home/r157428/.local/lib/python3.8/site-packages/nbclient/__init__.py", line 6, in <module>
from .client import NotebookClient, execute # noqa: F401
File "/home/r157428/.local/lib/python3.8/site-packages/nbclient/client.py", line 13, in <module>
from jupyter_client import KernelManager
ImportError: cannot import name 'KernelManager' from 'jupyter_client' (/home/r157428/.local/lib/python3.8/site-packages/jupyter_client/__init__.py)
```
The initial `quarto check` was okay, but the final `quarto check` was not okay since the initial python environment was replaced by the freshly created conda environment without jupyter.
> One quick solution to this issue with the python environments is to select the system python in Tools > Global Options > Python. That way one forces RStudio to use the system python to render the qmd file as well as run the python chunks inside the qmd file. If that was the original design plan then it should really be spelled out in the Quarto documentation. It's also very important to emphasize the role the **reticulate** R package is playing when running chunks of python code inside the Quarto document.
However, I came across another issue when running two consecutive python code chunks inside the qmd notebook. I added at the end of the **matplotlib demo** qmd from the Quarto documentation, the following python chunk:
````md
```{python}
x = np.linspace(-2,2,41)
y = np.exp(-x**2) * np.cos(2*np.pi*x)
plt.plot(x,y,alpha=0.4,label='Decaying Cosine',
color='red',linestyle='dashed',linewidth=2,
marker='o',markersize=5,markerfacecolor='blue',
markeredgecolor='blue')
plt.ylim([-2,2])
plt.legend()
plt.show()
```
````
The output of this python chunk was the following plot:
Here, the plot from the last python chunk, given above, was plotted on the top of the polar plot created by the previous python chunk. There is no issue when I render the entire qmd notebook.
Below is the complete qmd file I was playing with:
````
---
title: "matplotlib demo"
format:
html:
code-fold: true
jupyter: python3
---
For a demonstration of a line plot on a polar axis, see @fig-polar.
```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"
import numpy as np
import matplotlib.pyplot as plt
r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
subplot_kw = {'projection': 'polar'}
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```
```{python}
x = np.linspace(-2,2,41)
y = np.exp(-x**2) * np.cos(2*np.pi*x)
plt.plot(x,y,alpha=0.4,label='Decaying Cosine',
color='red',linestyle='dashed',linewidth=2,
marker='o',markersize=5,markerfacecolor='blue',
markeredgecolor='blue')
plt.ylim([-2,2])
plt.legend()
plt.show()
```
````
### The initial `quarto check` Output
```
/cloud/project$ quarto check jupyter
[β] Checking Python 3 installation....OK
Version: 3.8.10
Path: /usr/bin/python3
Jupyter: 4.11.1
Kernels: python3
[β] Checking Jupyter engine render....OK
```
### The final `quarto check` Output
```
/cloud/project$ quarto check jupyter
[β] Checking Python 3 installation....OK
Version: 3.8.13 (Conda)
Path: /cloud/home/r157428/.local/share/r-miniconda/envs/r-reticulate/bin/python
Jupyter: 4.11.1
Kernels: python3
(\) Checking Jupyter engine render..../home/r157428/.local/lib/python3.8/site-packages/jupyter_client/__init__.py:23: UserWarning: Could not import submodules
warnings.warn("Could not import submodules")
Traceback (most recent call last):
File "/opt/quarto/0.9.293/share/jupyter/jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "/opt/quarto/0.9.293/share/jupyter/notebook.py", line 14, in <module>
from nbclient import NotebookClient
File "/home/r157428/.local/lib/python3.8/site-packages/nbclient/__init__.py", line 6, in <module>
```
### `quarto tools check` Output
```
/cloud/project$ quarto tools check
[β] Reading Tool Data
Tool Status Installed Latest
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": 0,
"created_at": "2022-07-12T19:21:12Z",
"creator": "bkostadi",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1366,
"state": "open",
"title": "Issues with python env. when running a python chunk inside the qmd",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1366"
} |
By default the navbar title is created with a link to the root directory of the website (if the website is not using the file system). I believe this is because of the `js` function in `quarto-nav.js` which begins with the comment `// fixup index.html links if we aren't on the filesystem`.
Is it possible to allow an optional yaml configuration parameter provides users the ability to use either a custom url or specify something like `index.qmd`.
I tried to do something like this to `_quarto.yml`:
```
navbar:
title:
- href: index.qmd
text: mysite
```
But that didn't work. Nor could I could I find documentation that described this functionality. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-07-12T17:32:50Z",
"creator": "christian-million",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1396,
"state": "closed",
"title": "Option to Customize Navbar Title Link",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1396"
} |
### Bug description
Hello,
I've been working on a qmd file with Python only in VS Code (Windows 10.0.19044) for quite some time, but am suddenly running into `ModuleNotFoundError` errors when trying to render the qmd file (either via button or via terminal with `quarto render file.qmd`) despite no changes in my project folder.
I've noticed that pressing the render button starts either `quarto render file.qmd` or `quarto preview file.qmd` and I don't understand why this is or when to expect which command.
Strangely if I manually run `quarto preview file.qmd` via terminal it seems to fully render the report and after that I can use the render button and the manual render command?
Edit: it seems to be quite random as `quarto preview` can also lead to the error..?
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.11
Path: C:\Users\rindrakusuma\AppData\Local\Programs\Quarto\bin\
CodePage: unknown
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.4
Path: C:/Users/rindrakusuma/scoop/apps/python/current/python.exe
Jupyter: 4.10.0
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
[>] 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?
- [ ] 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.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 4,
"created_at": "2022-07-12T15:12:39Z",
"creator": "ifateri",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1365,
"state": "open",
"title": "Rendering qmd (button/command) suddenly leads to ModuleNotFoundError",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1365"
} |
### Bug description
This follows repo in #1361 and will use the same example. it also requires #1362 to work
First step:
Use branch from #1362 `bugfix/ext-paths`
Then:
````
quarto create-project website-with-ext --type website
cd .\website-with-ext\
quarto install extension quarto-ext/code-filename
mkdir more
````
then create a `index.qmd` in `more/`
````markdown
---
filters:
- code-filename
---
```{.python filename="matplotlib.py"}
import matplotlib.pyplot as plt
```
````
Then run `quarto render`
Look into `_site/site_libs`
````
> ls .\_site\site_libs\
Directory: C:\Users\chris\Documents\DEV_OTHER\ISSUES\quarto\website-with-ext\_site\site_libs
Mode LastWriteTime Length Name
---- ------------- ------ ----
d---- 12/07/2022 16:21 bootstrap
d---- 12/07/2022 16:21 clipboard
d---- 12/07/2022 16:21 quarto-html
d---- 12/07/2022 16:21 quarto-nav
d---- 12/07/2022 16:21 quarto-search
````
the dependencies from `code-filename` is not copied whereas it is correctly declared and inserted in HTML doc
https://github.com/quarto-ext/code-filename/blob/85dc809bb539711fa7767b19cac885e33e2664d1/_extensions/code-filename/code-filename.lua#L41-L45
I think the issue is in `copyResourceFile()`
https://github.com/quarto-dev/quarto-cli/blob/8baefa574e0b756ac22e05becad5b97ff33be5d6/src/project/project-resources.ts#L60-L68
* `srcFile` is `C:\Users\chris\Documents\DEV_OTHER\ISSUES\quarto\website-with-ext\more\../_extensions/quarto-ext/code-filename\code-filename.css`
* `rootDir` is `C:\Users\chris\Documents\DEV_OTHER\ISSUES\quarto\website-with-ext\more`
So extension is in the root of the project, but here the `rootDir` considered is the subfolder. So the `if` is TRUE and we do not copy it seems.
`copyResourceFile()` in question is called from
https://github.com/quarto-dev/quarto-cli/blob/1f06073c63a6abb12c4d8a169b5257833d522d1f/src/command/render/pandoc-dependencies-html.ts#L184-L191
Hope it helps pinpoint the problem, and hopefully I am in the right place.
| {
"assignee": null,
"comments": 3,
"created_at": "2022-07-12T14:30:41Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1363,
"state": "closed",
"title": "HTML dependencies from extension are not correctly copied when extension is used in subfolder",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1363"
} |
### Bug description
````
quarto create-project website-with-ext --type website
cd .\website-with-ext\
quarto install extension quarto-ext/code-filename
mkdir more
echo "---" > more/index.qmd
echo "filters:" >> more/index.qmd
echo " - code-filename" >> more/index.qmd
echo "---" >> more/index.qmd
quarto render
````
Content for `more/index.qmd` is really simple for the sake of the reprex
````
---
filters:
- code-filename
---
````
This is the issue we get
````
> quarto render
[1/3] about.qmd
[2/3] index.qmd
[3/3] more\index.qmd
Error running filter _extensions/quarto-ext/code-filename/code-filename.lua:
cannot open _extensions/quarto-ext/code-filename/code-filename.lua: No such file or directory
````
It seems we have an issue with Pandoc when an extensions filter is used in a subfolder.
The error above is from Pandoc. `pandoc` CLI is run in which environment ? It seems that the lua filter is not found because path is relative to where Pandoc is run and lua filter is not among the data files folder.
Using last dev version.
| {
"assignee": null,
"comments": 4,
"created_at": "2022-07-12T11:49:55Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1361,
"state": "closed",
"title": "Using filter extensions from document in subfolder makes pandoc error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1361"
} |
We now have tooltips for the code copy buttons with internationalized titles on hover and on click/success (yay!)β¦the only problem is, the tooltip delay is longer than the amount of time before the success icon/button changes back to its original form. So, there's no way for the "Copied!" tooltip to appear (see GIF, below)
The practice used elsewhere, e.g. in github issues (example below), [Bootstrap docs](https://getbootstrap.com/docs/5.1/components/tooltips/) (see any code chunk), in bookdown sites like [R for Data Science](library(tidyverse)), is to have no delay for the tooltip on success so that what happens is obvious/more perceivable (to put it in the accessibility POUR categories).
For code chunks on GitHub (use, e.g., the copy button below) the no-delay tooltip is _only_ on success, which might be preferable in order to avoid having too much motion/clutter.
```html
<p>This is a paragraph.</p>
<p>This is another paragraph.</p>
``` | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-07-12T11:35:11Z",
"creator": "batpigandme",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 1360,
"state": "closed",
"title": "Change tooltip delay for code-copy button",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1360"
} |
Currently, the code-copy button for HTML output gets its color from either `$text-muted` or `$link-color` depending on whether it's being hovered over from which an inline SVG is generated (as opposed to just the bi font symbol with color applied, which is totally fine):
https://github.com/quarto-dev/quarto-cli/blob/0a86a26aa9be10147d628c755f70fb889784018b/src/resources/formats/html/_quarto-rules-copy-code.scss#L15-L45
However, in cases where the code chunk syntax highlighting color is different to the background of the main site (e.g. on the mockup site I've been making here, I use `a11y-dark` for code chunks in a theme with a light bg: https://quartoand.me/syntax-highlighting-demo), it's pretty fiddly for the user to change the color, since they have to make the icon SVGs with a contrasting color manually. For example, for the page linked to above, I ended up adding the following to my custom.scss:
```scss
// fill color chosen to contrast with background of syntax-highlighting theme
/* code copy button hover */
pre.sourceCode:hover>.code-copy-button:hover>.bi::before {
background-image: url('data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="rgb(177, 183, 188)" viewBox="0 0 16 16"><path d="M4 1.5H3a2 2 0 0 0-2 2V14a2 2 0 0 0 2 2h10a2 2 0 0 0 2-2V3.5a2 2 0 0 0-2-2h-1v1h1a1 1 0 0 1 1 1V14a1 1 0 0 1-1 1H3a1 1 0 0 1-1-1V3.5a1 1 0 0 1 1-1h1v-1z"/><path d="M9.5 1a.5.5 0 0 1 .5.5v1a.5.5 0 0 1-.5.5h-3a.5.5 0 0 1-.5-.5v-1a.5.5 0 0 1 .5-.5h3zm-3-1A1.5 1.5 0 0 0 5 1.5v1A1.5 1.5 0 0 0 6.5 4h3A1.5 1.5 0 0 0 11 2.5v-1A1.5 1.5 0 0 0 9.5 0h-3z"/></svg>');
}
/* code copy button CHECK hover */
pre.sourceCode:hover>.code-copy-button-checked:hover>.bi::before {
background-image: url('data:image/svg+xml,<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="rgb(177, 183, 188)" viewBox="0 0 16 16"><path d="M13.854 3.646a.5.5 0 0 1 0 .708l-7 7a.5.5 0 0 1-.708 0l-3.5-3.5a.5.5 0 1 1 .708-.708L6.5 10.293l6.646-6.647a.5.5 0 0 1 .708 0z"/></svg>');
}
```
I certainly could've made/probably should make the above a bit more elegant by using my own variable for the fill color, but I'd still have to duplicate the code for generating the SVG that exists in [_quarto-rules-copy-code.scss](https://github.com/quarto-dev/quarto-cli/blob/0a86a26aa9be10147d628c755f70fb889784018b/src/resources/formats/html/_quarto-rules-copy-code.scss).
If you let me know what variable name I should use, I'd be happy to put in a PR for this. I realize this is quite niche, but, because there's no visible tooltip that indicates that the code has been copied (the icon changes to the check, and the _title_ changes to "Copied"), it's currently difficult to perceive what's happened after the button's been clicked if there's insufficient contrast. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-07-12T10:16:44Z",
"creator": "batpigandme",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 1359,
"state": "closed",
"title": "FR: Make code-copy-button colors configurable",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1359"
} |
I am following the example to create a new page on the website and things do not work as expected. Here is what it appears:
I copied and paste your example in your guide for creating a new page. No deviation from that. It works only if I create a new page naming it "About". For any other name the page looks as in the image I have attached | {
"assignee": null,
"comments": 5,
"created_at": "2022-07-12T06:20:34Z",
"creator": "ghost",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1358,
"state": "open",
"title": "New page does not work ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1358"
} |
When giscus is enabled, pages can be slow in loading while waiting for giscus to load. However giscus has a `data-loading="lazy"` option. On https://giscus.app this is described as:
> Loading of the comments will be deferred until the user scrolls near the comments container. This is done by adding loading="lazy" to the <iframe> element.
Currently quarto does not recognise the `data-loading` key. See here for the list of currently supported giscus keys: https://quarto.org/docs/reference/projects/websites.html#giscus
I propose to add this key. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-07-12T05:24:36Z",
"creator": "gustavdelius",
"is_pull_request": false,
"labels": [
"good-first-issue"
],
"locked": false,
"milestone": "v1.1",
"number": 1357,
"state": "closed",
"title": "For giscus implement `data-loading: lazy` to speed up page loading",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1357"
} |
Many academic journals in, eg, psychology require placing figures and tables at the end of the manuscript for review. I use the `endfloat` package to do this, as so:
```
header-includes:
- \usepackage{endfloat}
```
But I'm not a psychologist, and only very occasionally publish in journals that require moving the figures and tables around. So every time I have to mess around with a bunch of web searches until I find the magic combination of keywords that reminds me of `endfloat`.
So it would be nice to have a shortcut option, included in the Quarto docs, that might look like this:
```
endfloat: true
```
If the output format is PDF, this would simply include `\usepackage{endfloat}` in the header. And otherwise it would be ignored.
| {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-11T16:48:38Z",
"creator": "dhicks",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1352,
"state": "open",
"title": "[feature request] YAML shortcut for endfloat",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1352"
} |
I'm using Quarto for an HTML book and it seems https://quarto.org/docs/websites/website-tools.html#social-metadata works in that case too. Should the favicon docs be repeated in the book section? | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-11T10:05:00Z",
"creator": "maelle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1424,
"state": "closed",
"title": "Document that favicon can be used for HTML book projects too?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1424"
} |
I noticed that the shortcuts of css class in `remark.js` or `xaringan` slides are very convenient. Such as:
It can use
```
- ... .red[Text to be red] ...
```
to get a colored text.
It can use
```
.bold.center.green[Some bold, centered, and green text]
```
to get some bold, centered, and green text.
Is it possible to accomplish in `revealjs`? perhaps using lua plugin? | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-10T23:28:51Z",
"creator": "mingsu",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1350,
"state": "closed",
"title": "Shortcut of css styling in `revealjs` slides",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1350"
} |
### Bug description
LaTeX equations that include a new line code `\\` are not rendered on a new line:
When rendered as a PDF the "Inline math" format (`$math$`) works as it should and it uses the `\\` to print things on a new line. (I know using a new line command with "inline" code is illogical but it was useful to show the issue). The "Display Math" format (`$$math$$`) does not use the `\\` at all (and it needs to):
````
---
title: "Latex new line issue"
format: pdf
---
Showing Inline Math $1 < 2 \\ \neq -1\cdot 1 < -1 \cdot 2 \\ = -1 > -2$
or Display Math:
$$1 < 2 \\ \neq -1\cdot 1 < -1 \cdot 2 \\ = -1 > -2$$
````
When rendered to HTML neither the "Inline Math" nor "Display Math" formats use the requested new lines.
````
---
title: "Latex new line issue"
format: html
---
Showing Inline Math $1 < 2 \\ \neq -1\cdot 1 < -1 \cdot 2 \\ = -1 > -2$
or Display Math:
$$1 < 2 \\ \neq -1\cdot 1 < -1 \cdot 2 \\ = -1 > -2$$
````
The preview in the Studio IDE renders the LaTeX properly.
I am running:
```
R version 4.2.0 (2022-04-22)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.4, RStudio 2022.2.3.492
Locale: en_US.UTF-8 / en_US.UTF-8 / en_US.UTF-8 / C / en_US.UTF-8 / en_US.UTF-8
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_4.2.0 grDevices_4.2.0 highr_0.9
htmltools_0.5.2 jquerylib_0.1.4 jsonlite_1.8.0 knitr_1.39 magrittr_2.0.3
methods_4.2.0 R6_2.5.1 rappdirs_0.3.3 rlang_1.0.3 rmarkdown_2.14
sass_0.4.1 stats_4.2.0 stringi_1.7.6 stringr_1.4.0 tinytex_0.40
tools_4.2.0 utils_4.2.0 xfun_0.31 yaml_2.3.5
Pandoc version: 2.17.1.1
```
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 1.0.7
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
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Up to date v2022.07 v2022.07
WARNING: TeX Live not on path.
### 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": "2022-07-10T14:20:32Z",
"creator": "RaymondBalise",
"is_pull_request": false,
"labels": [
"upstream"
],
"locked": false,
"milestone": null,
"number": 1348,
"state": "closed",
"title": "LaTeX not adding new line",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1348"
} |
```% quarto tools check
[β] Inspecting tools
ERROR: TypeError: Specifier not found in cache: "https://deno.land/x/[email protected]/directories.ts", --cached-only is specified.
at file:///Applications/quarto/bin/vendor/deno-land/x/puppeteer@9-0-2/vendor/puppeteer-core/vendor/cache.ts:1:26```
| {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-10T03:33:53Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1344,
"state": "closed",
"title": "Fix import map to reference vendored cache library",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1344"
} |
Coconut (https://coconut.readthedocs.io/en/latest/FAQ.html) seems to add very useful functional programming tools to python and can be used as a Jupyter kernel.
It could be promising to use this together with R in a Rmd/qmd-File. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-07-09T06:42:23Z",
"creator": "henningsway",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1343,
"state": "open",
"title": "Feature-Idea: Adding support for coconut (functional python dialect)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1343"
} |
I mostly use quarto with a particular conda environment and for some reason even when I run it after activating the environment, it still runs the default python. Is there some frontmatter to force a particular python interpreter?
Is there a place to read up on all frontmatter options? I couldn't seem to find it in the user guide or reference page. | {
"assignee": null,
"comments": 7,
"created_at": "2022-07-08T19:10:05Z",
"creator": "amichuda",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1341,
"state": "closed",
"title": "YAML frontmatter for python path",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1341"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1310
<div type='discussions-op-text'>
<sup>Originally posted by **harrelfe** July 6, 2022</sup>
I moved a book to a new directory, removed _freeze, re-started a book project, and rendered all chapters. All chapters look fine except for one, using `Quarto` 0.9.648. The directory `_book/chaptername_files` is empty even though there were no execution errors.
I haven't changed any of the chapter script. I'm sorry I can't produce a short example.
**UPDATE** The chapter starts with two `mermaid` charts. When I remove those two chunks the graphs render as they are supposed to.
**UPDATE 2** When I put the chapter as a self-contained article there is no problem with the figures. The `book` environment seems to have a problem.
Here is a minimal failing example book: https://hbiostat.org/attach/btest.zip
**UPDATE 3** I had to go all the way back to `Quarto` 0.9.560 to get the figures rendered when preceded by a `mermaid` chunk.
</div> | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-07-08T16:19:59Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "1.0",
"number": 1340,
"state": "closed",
"title": "Graphics images not being created in one book chapter",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1340"
} |
```
---
title: "Untitled"
subtitle: "[**Example**](https://www.example.com/)"
author: "[**Example**](https://www.example.com/)"
---
```
A Quarto document using the above YAML will render the markdown used in the `subtitle` field but not the `author` field. (Using the same YAML for an RMarkdown document will render the markdown from both fields.)
***
```
[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: 3.7.3
Path: /Library/Developer/CommandLineTools/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: 4.2.0
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
``` | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-07-08T16:17:46Z",
"creator": "daviddalpiaz",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1339,
"state": "closed",
"title": "YAML author field does not allow markdown",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1339"
} |
### Bug description
Trying to run
````powershell
β― quarto use tempate quarto-journals/plos
````
shows no output at all. No message no error. I think it does nothing (hopefully).
This is a typical typo in command line argument (missing `l` for `template`), but no message makes it not clear that there was an issue.
cc @dragonstyle
### `quarto check` Output
````powershell
β― 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: 4.2.1
Path: C:/PROGRA~1/R/R-42~1.1
LibPaths:
- C:/Users/chris/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.1/library
rmarkdown: 2.14.3
[>] Checking Knitr engine render......OK
````
### `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": null,
"comments": 0,
"created_at": "2022-07-08T11:53:07Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1336,
"state": "closed",
"title": "Give some hints or at least useful error when mispelled usage in CLI like `quarto use`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1336"
} |
### Bug description
In https://mlr3book.mlr-org.com/ we see that the GH icon which is populated by defining `repo-url` is prefixed with the CNAME entry (which lives in the [gh-pages](https://github.com/mlr-org/mlr3book/tree/gh-pages) branch).
This only happens when deploying via CI. In local previews, the link is correct (i.e. does not contain the CNAME prefix).
Repo: https://github.com/mlr-org/mlr3book
Workflow: https://github.com/mlr-org/mlr3book/blob/main/.github/workflows/build-book.yml
cc https://github.com/mlr-org/mlr3book/issues/375
### `quarto check` Output
quarto v0.9.655 during the latest CI run
### `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?
- [ ] 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": "jjallaire",
"comments": 1,
"created_at": "2022-07-08T07:55:29Z",
"creator": "pat-s",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1335,
"state": "closed",
"title": "book: GitHub icon link set by `repo-url` is prefixed with CNAME entry",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1335"
} |
I've created figures using R and mermaid. The outcomes for the figures differs and I suspect neither meets WCAG.
Both code blocks use label, fig-cap, and fig-alt.
The R graph does get an alt tag, created using #| fig-alt: ...
It is read aloud by my screen reader when I get to the graphic's placement in the text.
However, the caption is not read aloud by either screen reader I've tried.Initially, I thought it was because the caption is being embedded int he image file, but upon inspection of the png in the figures subfolder, the image does not include the caption.
WRT the mermaid flow chart: I do not get a caption with the same findings as for the R graph. I do not though even get told the graphic exists in my html page by the screen readers nor is the alt tag text read aloud. I have tried using hte default presentation of the mermaid graph, as well as explicitly choosing to create png and svg; the outcomes remain the same.
I've really appreciated the inclusion of fig.alt in knitr, as an opportunity to get more information than can be imparted in a figure's caption.
How can I get the captions included as regular text as was the norm with rmarkdown::render()?
Is there a switch to add to the main YAML? If so, I haven't found it documented. If not, can I request that one be created.
Thanks,
Jonathan
| {
"assignee": null,
"comments": 7,
"created_at": "2022-07-08T07:25:30Z",
"creator": "ajrgodfrey",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1346,
"state": "open",
"title": "quarto embeds captions in figures",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1346"
} |
### Bug description
Despite `quarto render --help`, `quarto serve --help`, etc. work for most sub-commands, it does not work for:
* [ ] `quarto preview --help`
* [ ] `quarto run --help`
Specifically,
```sh
$ quarto preview --help
ERROR: /home/hb is not a website or book project
$ quarto run --help
ERROR: quarto run: script '--help' not found
```
This is on an up-to-date Ubuntu 20.04 machine.
Possibly related to https://github.com/quarto-dev/quarto-cli/issues/598
### `quarto check` Output
```
$ quarto check
[β] Checking Quarto installation......OK
Version: 0.9.644
Path: /home/hb/shared/software/CBI/quarto-0.9.644/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: /home/hb/shared/software/CBI/R-4.2.1-gcc9/lib/R
LibPaths:
- /home/hb/R/x86_64-pc-linux-gnu-library/4.2-CBI-gcc9
- /home/hb/R/x86_64-pc-linux-gnu-library/4.2-CBI-gcc9/_bioc-3.15
- /home/hb/shared/software/CBI/R-4.2.1-gcc9/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
$ quarto tools check
(-) 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 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": "jjallaire",
"comments": 5,
"created_at": "2022-07-07T21:15:43Z",
"creator": "HenrikBengtsson",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1333,
"state": "closed",
"title": "quarto <subcommand> --help does not work for 'preview' and 'run'",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1333"
} |
{
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-07-07T17:11:10Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1315,
"state": "open",
"title": "transfer quarto-web issues to quarto-cli",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1315"
} |
|
Hi I have an issue rendering the .qmd pdf.
Sessioninfo is attached as well as showing you , that there is no way i can update the tlmgr manager
Hi, Windows PowerShell
Copyright (C) Microsoft Corporation. All rights reserved.
Try the new cross-platform PowerShell https://aka.ms/pscore6
PS C:\Users\Username> tlmgr update --all
tlmgr.pl: package repository https://ctan.math.illinois.edu/systems/texlive/tlnet (verified)
tlmgr.pl: no updates available
PS C:\Users\Username>
| {
"assignee": null,
"comments": 20,
"created_at": "2022-07-07T14:21:21Z",
"creator": "HomeStayMom",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1312,
"state": "closed",
"title": "issue with updating tlmgr updating existing packages",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1312"
} |
### Bug description
According to <https://quarto.org/docs/authoring/title-blocks.html#metadata-labels>, `affiliation-title` can be used to change the block title, but it does not work.
```qmd
---
title: "Untitled"
lang: fr
author:
- name: "MickaΓ«l"
affiliation: "Institut Pasteur de Lille"
affiliation-title: "Affiliation"
author-title: "Test"
format: html
---
```
while using `language` we can override the block title.
```qmd
---
title: "Untitled"
lang: fr
author:
- name: "MickaΓ«l"
affiliation: "Institut Pasteur de Lille"
author-title: "Test"
language:
title-block-affiliation-single: "Affiliation"
title-block-affiliation-plural: "Affiliations"
format: html
---
```
OS: MacOS (arm64)
Quarto: 0.9.646
IDE: VSCode (latest)
Repo for reproducible example: https://github.com/mcanouil/quarto-issues/tree/main/quarto-cli-1306
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 0.9.646
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
```
Download 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 Not installed --- v2022.07
```
| {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-07-06T20:50:26Z",
"creator": "mcanouil",
"is_pull_request": false,
"labels": [
"bug",
"verify-fixed"
],
"locked": false,
"milestone": "1.0",
"number": 1306,
"state": "closed",
"title": "`affiliation-title` does not work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1306"
} |
Repro:
---
title: "Untitled"
format: html
editor: visual
---
Hello, an hr.
---
Hello, another thing.
---
And what about this?
`Hello, another thing` gets picked up as YAML by RStudio, and VS Code, but _not_ by our CLI:
<img width="267" alt="image" src="https://user-images.githubusercontent.com/285675/177629161-4b9d24ab-ffca-4c9c-ae21-a0bc1560dc7c.png">
| {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-06T19:36:48Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1304,
"state": "closed",
"title": "Don't interpret text between `---` HRs as yaml",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1304"
} |
### Bug description
When the notebook has latex equations inside a Markdown cell in Jupyter Lab equations do not appear in the HTML converted by quarto.
Here is what I get in the html
and here is the relevant code:
There are various versions of this equation, depending on the application. For the point I want to make here, a conventional approach more than suffices. In this case, and in order to link inflation, interest rates, consumption and income and substitution effects, I would assume that in the aggregate the path of consumption follows the following rule (See [here](https://core.ac.uk/download/pdf/6377146.pdf) or [here](https://www.thijsvanrens.com/macro/SE_IE_note.pdf) for a simple example)
<!--
(https://www.bankofengland.co.uk/-/media/boe/files/events/2021/november/advanced-analytics-conference/diana-gabrielyan--poster-session-paper.pdf?la=en&hash=03B7D5734038D4114CE25447699B4690BFF65750)):
-->
$$
E_{t} \Delta \overline{ c_{t+1}}=\sigma \widehat{r_{t}}
$$
where
$$
\Delta \overline{ c_{t+1}} = \log(c_{t+1}) - \log(c_{t}) \quad ( \text{real consumption growth})
$$
$$
\widehat{r_{t}} = \log(r_{t}) - \log(r^*)
$$
$$
\text{and} \quad r_{t} = i_{t} - \pi_{t+1} \quad ( \text{real risk-free/fund rate with } r^* \equiv \text{long-run values})
$$
``` | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-07-06T18:51:17Z",
"creator": "ghost",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1303,
"state": "closed",
"title": "Failure to convert equations ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1303"
} |
{
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-07-06T17:21:49Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "1.0 Chores",
"number": 1301,
"state": "closed",
"title": "distinguish v1.0 builds vs. daily builds",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1301"
} |
|
{
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-07-06T17:21:08Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "1.0",
"number": 1300,
"state": "closed",
"title": "change version number to v1.0",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1300"
} |
|
### Bug description
_No response_
### `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": 0,
"created_at": "2022-07-06T17:16:41Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1299,
"state": "closed",
"title": "make extension and publish commands visible (hide tools command?)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1299"
} |
The setting collapse="true" **does not** work in a revealjs presentation.
See code below:
:::{.callout-caution **collapse="true**"}
## Expand To Learn About Collapse
This is an example of a 'folded' caution callout that can be expanded by the user. You can use `collapse="true"` to collapse it by default or `collapse="false"` to make a collapsible callout that is expanded by default.
::: | {
"assignee": null,
"comments": 6,
"created_at": "2022-07-06T15:15:58Z",
"creator": "meersel",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs",
"callouts"
],
"locked": false,
"milestone": "Future",
"number": 1328,
"state": "open",
"title": "collapse setting in callout block in a revealjs presentation not working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1328"
} |
### Bug description
Create a book project
````
quarto create-project test-quarto-book --type book
````
Add classes une header like this in `index.qmd`
````
# Preface {.unnumbered .unlisted}
````
Render to PDF -> the classes are not correctly parsed by Pandoc and the curly braces part is taken as is.
in tex
````tex
\chapter*{Preface \{.unnumbered,.unlisted\}}\
````
I am still trying to figure out where this is can happen in our filters.
It only happens in book project. I can reproduce within a single document
This is using last dev version 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": "cderv",
"comments": 0,
"created_at": "2022-07-06T14:58:25Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1297,
"state": "closed",
"title": "Adding more that one class on header in book is not parsed correctly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1297"
} |
### Bug description
**Description**: the graphviz diagrams using _dot_ engine are rendered incorrectly - get chopped off at the bottom - if the outputs are too long in size. Previewing is unaffected.
**How to reproduce?**: Draw a long graphviz
```dot
//| label: pathology
//| fig-cap: Pathology of TBM
//| fig-align: center
digraph pathology {
Aerosol -> Lung
Lung:e -> Lung:e
Lung -> Blood
Blood -> {Organ:n CNS}
Blood:w -> Lung:w
Organ:s -> Organ:s
CNS -> Latent
CNS -> Rich:n
Latent -> Rich:n
Rich -> Subarchnoic
Subarchnoic:s -> Subarchnoic:n
}
```
quarto version 0.9.644
dot - graphviz version 3.0.0 (20220226.1711)
Environment/IDE: VSCode 1.68.1/darwin x64 21.5
No R computation involved yet.
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 21,
"created_at": "2022-07-06T13:47:06Z",
"creator": "trinhdhk",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "Future",
"number": 1296,
"state": "closed",
"title": "graphviz diagrams are rendered incorrectly ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1296"
} |
### Bug description
When exporting to PDF, and `keep-tex: true` and `output-dir: "outdir"` are both set in the relevant YAML, the `.tex` file remains in the working directory, even after the `.pdf` file is moved to `outdir`.
## Reprex
1. Create a new Quarto project, with the following contents in the `_quarto.yml` file:
```
project:
title: "test"
output-dir: "outdir"
```
2. Create a `test.qmd` file with the following contents:
```
---
title: "test"
format:
pdf:
keep-tex: true
---
Hello
```
3. Render the project. Observe that `test.pdf` is in the `outdir` subdirectory, but `test.tex` remains in the project directory.
## System Stats
Results of `quarto check`:
```
[β] Checking Quarto installation......OK
Version: 0.9.637
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.6 (Conda)
Path: /Users/connor/opt/miniforge/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda 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-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
RStudio Version `2022.02.3 Build 492`. Session Info:
```
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.1 tools_4.2.1
```
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-07-06T02:25:10Z",
"creator": "connorp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1294,
"state": "open",
"title": "TeX file is not moved to output-dir",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1294"
} |
# Bug description
When my working directory on my Mac is within a Google Drive folder that is shared with my Google Drive account (reached via shortcut), Quarto does not respect the `execute-dir: project` option. This can cause problems with rendering if you have referenced other files assuming the main project directory is the working directory. I suspect this is a larger issue than just the `execute-dir` option (Google Drive does weird things with these shortcut folders), and it might not even be fixable on your end, but I wanted to flag it just in case. Also, just using `execute-dir: file` and changing all my file references isn't a great option, because then the code doesn't work interactively, when my working directory IS the project directory.
## Reprex
1. Install the Google Drive desktop app for Mac
2. Create a Quarto project within a directory that is shared with your google drive account (access it by creating a shortcut to that directory in your Google Drive 'My Drive' folder), add the following to the `_quarto.yml` file:
```
project:
title: "test"
execute-dir: project
```
4. To demonstrate the issue, create a subdirectory called `code` within the project folder. Create two files within this subdirectory, with the following contents:
test.R
```
print("hello, world")
```
test.qmd
````
---
title: "test"
format: html
execute-dir: project
---
```{r}
source("code/test.R")
```
````
5. Attempt to render this `.qmd` file (or project). The render will fail with the following error:
```
Quitting from lines 8-9 (test.qmd)
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
Calls: .main ... eval_with_user_handlers -> eval -> eval -> source -> file
Execution halted
```
## System Stats
Results of `quarto check`:
```
[β] Checking Quarto installation......OK
Version: 0.9.637
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.6 (Conda)
Path: /Users/connor/opt/miniforge/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda 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-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
RStudio Version `2022.02.3 Build 492`. Session Info:
```
R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.1 tools_4.2.1
```
# 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-07-06T01:39:48Z",
"creator": "connorp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1293,
"state": "open",
"title": "Quarto does not respect execute-dir in Google Drive Shared Directories",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1293"
} |
### Bug description
[This repository](https://github.com/hadley/r-pkgs/pull/819) builds incorrectly on Netlify's deployment when their asset optimization pipeline is turned on.
There's probably an interaction between our own optimization and minification and Netlify's.
We should at least add a warning in our netlify deploy docs.
This was run on v0.9.640 which GHA CI.
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": 6,
"created_at": "2022-07-05T15:55:10Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1290,
"state": "closed",
"title": "netlify's asset optimization pipeline interacts badly with quarto's",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1290"
} |
### Bug description
I developed a qmd document in linux (popOS 22.10) but recently switched to a windows machine. On linux, the qmd document renders without issue. When running the same document in windows, the following issues don't work:
1. Title does not appear
2. Table of contents does not appear
3. Font styles from the styling template are not correct
4. Bibliography (.bib) and csl documents do not generate a references page.
The text and figures within the quarto document work as expected. Is there something specific I should be doing in windows that I didn't have to do in linux?
````
title: "Project Title"
format:
docx:
reference-doc: styling_template.docx
toc: true
toc-title: Table of Contents
fig-cap-location: bottom
tbl-cap-location: top
bibliography: references.bib
csl: apa.csl
````
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-07-05T15:03:07Z",
"creator": "SolarDifference",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1288,
"state": "open",
"title": "Document renders correctly in linux but not in windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1288"
} |
Request to have built-in tabbed code blocks as well as terminal/file blocks with the ability to add a title:
<img width="614" alt="image" src="https://user-images.githubusercontent.com/31460023/177347630-3b351a02-83bc-4f4e-ad2a-1a6a2656611d.png">
<img width="608" alt="image" src="https://user-images.githubusercontent.com/31460023/177347657-d97aaf05-d6f4-4459-9369-3c18bc86c1e3.png">
MkDocs - Material examples:
Tabs example:
```
=== "RHEL 8"
```
$ curl -O https://cdn.rstudio.com/connect/{{ vars.connect.rsc.short_version }}/rstudio-connect-{{ vars.connect.rsc.full_version }}.el8.x86_64.rpm
$ sudo yum install rstudio-connect-{{ vars.connect.rsc.full_version }}.el8.x86_64.rpm
```
=== "RHEL/CentOS 7"
```
$ curl -O https://cdn.rstudio.com/connect/{{ vars.connect.rsc.short_version }}/rstudio-connect-{{ vars.connect.rsc.full_version }}.el7.x86_64.rpm
$ sudo yum install rstudio-connect-{{ vars.connect.rsc.full_version }}.el7.x86_64.rpm
```
=== "Amazon Linux 2"
```
$ curl -O https://cdn.rstudio.com/connect/{{ vars.connect.rsc.short_version }}/rstudio-connect-{{ vars.connect.rsc.full_version }}.amazonlinux2.x86_64.rpm
$ sudo yum install rstudio-connect-{{ vars.connect.rsc.full_version }}.amazonlinux2.x86_64.rpm
```
=== "Ubuntu 22.04"
```
$ sudo apt-get install gdebi-core
$ curl -O https://cdn.rstudio.com/connect/{{ vars.connect.rsc.short_version }}/rstudio-connect_{{ vars.connect.rsc.full_version }}~ubuntu22_amd64.deb
$ sudo gdebi rstudio-connect_{{ vars.connect.rsc.full_version }}~ubuntu22_amd64.deb
```
=== "Ubuntu 20.04"
```
$ sudo apt-get install gdebi-core
$ curl -O https://cdn.rstudio.com/connect/{{ vars.connect.rsc.short_version }}/rstudio-connect_{{ vars.connect.rsc.full_version }}~ubuntu20_amd64.deb
$ sudo gdebi rstudio-connect_{{ vars.connect.rsc.full_version }}~ubuntu20_amd64.deb
```
Code/file block with title example:
```
``` bash title="Terminal"
sudo systemctl stop rstudio-pm
sudo systemctl start rstudio-pm
```
``` | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-07-05T14:15:06Z",
"creator": "AshleyHenry15",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1287,
"state": "closed",
"title": "Built-in tabbed code blocks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1287"
} |
### Bug description
The below produces an error because the affiliation fields are identical.
```
affiliations:
- id: aff1
name: Affiliation Dept/Program/Center, Institution Name
city: City
state: State
country: Country
- id: aff2
name: Affiliation Dept/Program/Center, Institution Name
city: City
state: State
country: Country
- id: aff3
name: Affiliation Dept/Program/Center, Institution Name
city: City
state: State
country: Country
```
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, self-contained, and reproducible example?
- [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": "dragonstyle",
"comments": 0,
"created_at": "2022-07-05T14:08:29Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1286,
"state": "closed",
"title": "Error when affiliations are identical other than id",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1286"
} |
### Bug description
This currently does not work and yields an obscure error message:
```
Quitting from lines 614-656 (man.Rmd)
Error in `if (options$fig.show == "hide") ...`:
! argument is of length zero
```
Note that this _does_ work in R Markdown so is something we should definitely support.
cc @hadley
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, self-contained, and reproducible example?
- [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": 2,
"created_at": "2022-07-05T12:58:38Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1285,
"state": "closed",
"title": "support knitr::include_graphics in inline r code",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1285"
} |
### Bug description
When I created a Quarto book in "docx" format with a chapter with codes from "table1" and "gtsummary" packages to construct summary tables, I failed to make it and saw the following error messages.
**Error in flextable_to_rmd(x, bookdown = is_bookdown, pandoc2 = pandoc2, :
pandoc version >= 2.0 required for flextable rendering in docx
Calls: .main ... knit_print -> knit_print.flextable -> flextable_to_rmd
Execution halted**
But when I created, using Rmd file, not qmd file as in quarto book, a separate word document with codes from "table1" and "gtsummary" packages to construct summary tables, I make it successfully.
How can I solve the problem in quarto qmd system?
Thanks
Ko Ko Zaw
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, self-contained, and reproducible example?
- [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": "2022-07-05T12:22:24Z",
"creator": "zawkzaw",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1284,
"state": "closed",
"title": "failed to make tables by \"table1\" and \"gtsummary\" packages in quarto book project ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1284"
} |
When rendering pdf from Quarto I get an error, and the following output in the pdf-log.
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex 2022.7.3) 3 JUL 2022 21:31
entering extended mode
restricted \write18 enabled.
%&-line parsing enabled.
**write_pdf.tex
(./write_pdf.tex
LaTeX2e <2022-06-01> patch level 3
L3 programming layer <2022-06-16>
**! LaTeX Error: File `scrartcl.cls' not found.**
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: cls)
Enter file name:
! Emergency stop.
<read *>
l.10 \usepackage
{amsmath,amssymb}^^M
| {
"assignee": null,
"comments": 7,
"created_at": "2022-07-03T19:55:47Z",
"creator": "ca-signorelli",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1281,
"state": "closed",
"title": "Rendering pdf - File `scrartcl.cls' not found",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1281"
} |
### Bug description
Same problem with markdown(https://github.com/microsoft/vscode/issues/146610)
The bug of mrkdown was fixed by [babakks](https://github.com/babakks).
So I think the quarto would be fixed easily. Thanks.
Please refer to the following code.
(https://github.com/microsoft/vscode/pull/147239/commits/23b2e7b41ce9492978fc0079c377dff66942eb03)
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, self-contained, and reproducible example?
- [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": 1,
"created_at": "2022-07-03T03:32:58Z",
"creator": "jjyunnn",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1280,
"state": "closed",
"title": "Fix single tilde (~) strikethrough parsing",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1280"
} |
### Bug description
When `output-location` is not specified for an R chunk, the resulting figure fills up the available space and is resized automatically.
When `output-location: fragment`, the figure is not resized, potentially extending beyond the slide.
I would expect the figure sizes to be the same for these two situations since `fragment` is supposed to just delay the figure display.
An example of this can be found in the embedded slide deck at https://mine-cetinkaya-rundel.github.io/quarto-tip-a-day/posts/05-output-location/.
- Quarto: I'm using dev quarto: 99.9.9
- RStudio: RStudio 2022.07.0-preview+544 "Spotted Wakerobin" Preview (3a56d20250c52c4b1690d909a00f17e4b4627e54, 2022-06-27) 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-07-02T22:23:13Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1279,
"state": "open",
"title": "Figure sizing is inconsistent between default and fragment output location in revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1279"
} |
### Bug description
The two options below should give the same output but they don't:
- Option 1: Set `echo: fenced` at document level:
````
---
format: html
execute:
echo: fenced
---
No other chunk options:
```{r}
1 + 1
```
With other chunk options:
```{r}
#| label: addition
1 + 1
```
````
Here is the output for Option 1:
<img width="682" alt="Output of document with source code given above, with annotation showing an empty line at the beginning of the first chunk." src="https://user-images.githubusercontent.com/5965649/177011414-3268746e-a120-49e7-b907-160e1cc6cfd2.png">
- Option 2: Set `echo: fenced` at chunk level:
````
---
format: html
---
No other chunk options:
```{r}
#| echo: fenced
1 + 1
```
With other chunk options:
```{r}
#| echo: fenced
#| label: addition
1 + 1
```
````
Here is the output for Option 2:
<img width="684" alt="Output of document with source code given above" src="https://user-images.githubusercontent.com/5965649/177011447-54840013-f27a-44b7-b569-967991941690.png">
I think the second output looks right, there shouldn't be an empty line in the chunk when no other chunk options are specified.
- Quarto: I'm using dev quarto: 99.9.9 (unfortunately `quarto check` is giving me an error right now)
- RStudio: RStudio 2022.07.0-preview+544 "Spotted Wakerobin" Preview (3a56d20250c52c4b1690d909a00f17e4b4627e54, 2022-06-27) 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-07-02T18:01:56Z",
"creator": "mine-cetinkaya-rundel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1278,
"state": "closed",
"title": "Setting echo: fenced at document level yaml creates empty line in chunks with no other options",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1278"
} |
Repro:
---
title: Button Style Inconsistency
---
```{ojs}
viewof foo = Inputs.button("OJS Button")
```
<button>Plain Button</button>
<img width="622" alt="image" src="https://user-images.githubusercontent.com/285675/177009216-bd142708-e6b3-4071-8595-9f9fb4f2022b.png">
Yuck. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-02T16:46:51Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"ojs-engine"
],
"locked": false,
"milestone": "Future",
"number": 1276,
"state": "closed",
"title": "CSS for buttons is inconsistent",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1276"
} |
### Bug description
Hi Quarto Devs
I've been loving using the tool so far, but have had some hiccups with the PDF generation.
I'm currently using it to write summaries for university and recently wanted to change the section, subsection, etc. -styles with the `titlesec` package. This doesn't seem to work directly with the following added packages.
```latex
\usepackage{multicol}
\usepackage[german]{babel}
\usepackage[utf8]{inputenc}
\usepackage{titlesec}
```
Which gave following output:
```
compilation failed- error
Argument of \paragraph has an extra }.
<inserted text>
\par
l.1641 \ttl@extract\paragraph
```
I have googled the issue and found this stackoverflow discussion: https://stackoverflow.com/questions/42916124/not-able-to-use-titlesec-with-markdown-and-pandoc, which indicates that a pandoc configuration is required. I don't know how to do this and wanted to know if you could help out.
---
```
[>] Checking Quarto installation......OK
Version: 0.9.637
Path: C:\tools\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.2
Path: C:/.../AppData/Local/Programs/Python/Python310/python.exe
Jupyter: 4.9.2
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/
```
And Operating System
```
OS Name: Microsoft Windows 10 Pro
Version: 10.0.19044 Build 19044
System Type: x64-based PC
```
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-07-01T21:22:26Z",
"creator": "joelvonrotz",
"is_pull_request": false,
"labels": [
"bug",
"invalid"
],
"locked": false,
"milestone": null,
"number": 1273,
"state": "closed",
"title": "Latex Package 'titlesec'",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1273"
} |
### Bug description
Hello
I am writing a quarto book and I need to integrate external pdf files into the quarto book.
How can I do this?
Best wishes
Ko Ko Zaw
| {
"assignee": null,
"comments": 3,
"created_at": "2022-07-01T18:47:35Z",
"creator": "zawkzaw",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1270,
"state": "closed",
"title": "how to insert pdf file in quarto book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1270"
} |
Repro:
---
title: "sidebyside"
format: pdf
editor: visual
keep-tex: true
---
```{r}
#| layout-ncol: 2
#| layout-valign: bottom
#| fig-cap: "A plot"
#| tbl-cap: "A table"
library(knitr)
# plot on the left
plot(cars)
# table on the right
kable(head(cars))
```
Note the duplicated caption on the figure:
<img width="612" alt="image" src="https://user-images.githubusercontent.com/285675/176945999-376451f8-2e00-41cb-9c9c-720a528ae534.png">
| {
"assignee": null,
"comments": 0,
"created_at": "2022-07-01T17:52:14Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1269,
"state": "open",
"title": "Repeated figure caption when figure and table captions are mixed",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1269"
} |
We should have a schema that enables completion and validation for `_extension.yml`. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-01T15:55:47Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"yaml-validation"
],
"locked": false,
"milestone": "v1.1",
"number": 1268,
"state": "closed",
"title": "add yaml intelligence for _extension.yml",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1268"
} |
https://stackoverflow.com/questions/72799825/side-by-side-caption-positions-of-figure-and-table
There's an easier repro:
---
title: "sidebyside"
format: pdf
---
```{r}
#| cap-location: bottom
#| tbl-cap: "A table"
library(knitr)
kable(head(cars))
```
https://quarto.org/docs/reference/formats/pdf.html#layout claims `cap-location` should work, but it's not. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-01T14:51:53Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1267,
"state": "closed",
"title": "kable does not see `cap-location` or `tbl-cap-location`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1267"
} |
### Bug description
I'm getting a `YAMLException: bad indentation of a mapping entry` error when using a `:` inside `paste()` or `glue()` in `fig-`/`tbl-cap`.
I'm using RStudio 4.2.0 with Quarto v. 0.9.624 on macOS 12.3.1.
I'm pretty sure it worked a few weeks ago with an older version of Quarto.
``````
---
format: pdf
---
```{r}
#| echo: false
#| fig-cap: !expr paste("foo: bar")
plot(1)
```
``````
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-01T11:09:43Z",
"creator": "arnaudgallou",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1265,
"state": "closed",
"title": "Captions: colon inside `paste()` leads to `bad indentation of a mapping entry` error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1265"
} |
### Bug description
The following file `quote.qmd` contains a quote as suggested at https://stackoverflow.com/questions/2002120/citing-the-author-of-a-blockquote-using-markdown-syntax
```
---
title: "Famous Quote"
format: revealjs
---
> "God doesn't play dice."
>
> -- <cite>Albert Einstein</cite>
```
When rendering with pandoc like
pandoc -t revealjs -s -o quote.html quote.qmd
the output is as expected:
However, when rendering the same document with quarto the `<cite>` tags seemed to be ignored and quote and author appear in one line.
quarto render quote.qmd
Interestingly when rendered to plain html (`format: html`) instead of reveal-js (`format: revealjs`) the problem does not occur
This happens with quarto 0.9.592 and pandoc 2.18 on Mac OS X 10.15.7 .
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-06-30T21:40:39Z",
"creator": "asmaier",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1264,
"state": "closed",
"title": "reveal-js: Blockquotes rendered differently from pandoc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1264"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1253
<div type='discussions-op-text'>
<sup>Originally posted by **fuhrmanator** June 29, 2022</sup>
My book project hits this bug https://github.com/denoland/deno/issues/13408 when I do `quarto render --to html` -- it's happening while doing the last HTML file, which is the Bibliography. All the chapters look OK.
If I remove half of the chapters, it finishes completely.
Any ideas about how to proceed? The github issue above went stale because people weren't able to reproduce it, but it seems with my repo it's possible 100% of the time. Right now it's a private repo, but I will soon make it public. </div> | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2022-06-30T17:20:17Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1263,
"state": "closed",
"title": "Out of Memory when rendering to HTML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1263"
} |
Repro on _quarto.yml on quarto-web contents lists | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-06-30T17:12:32Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "1.0",
"number": 1262,
"state": "closed",
"title": "completion through string+object is insisting on object",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1262"
} |
### Bug description
Let's say I want to change `highlight-style` for reveal
````yaml
format:
revealjs:
highlight-style: #<-- won't be suggested in auto completion
````
Other example
````yaml
format:
pdf:
pdf-engine: #<-- not suggested by auto completion
````
Not sure which is the pattern.
Using latest quarto (d5203c660d293ae3d3ee1b1055da37b74ec4acf0) on Windows 10
````
β― 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...........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
````
````
> RStudio.Version()
$citation
To cite RStudio in publications use:
RStudio Team (2022). RStudio: Integrated Development Environment for R. RStudio, PBC, Boston, MA URL http://www.rstudio.com/.
Une entrΓ©e BibTeX pour les utilisateurs LaTeX est
@Manual{,
title = {RStudio: Integrated Development Environment for R},
author = {{RStudio Team}},
organization = {RStudio, PBC},
address = {Boston, MA},
year = {2022},
url = {http://www.rstudio.com/},
}
$mode
[1] "desktop"
$version
[1] β2022.7.0.545β
$long_version
[1] "2022.07.0-preview+545"
$release_name
[1] "Spotted Wakerobin"
````
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": 2,
"created_at": "2022-06-30T15:42:29Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "1.0",
"number": 1260,
"state": "closed",
"title": "Autocompletion is not correctly showing all possible options",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1260"
} |
### Bug description
In-text citation as shown at the end of the [Citation syntax](https://quarto.org/docs/authoring/footnotes-and-citations.html#sec-citations) section doesn't seem to work for citation style referencing citations from 1 to n (e.g. Science, PNAS, Nature, etc.). An example can be found [here](https://github.com/arnaudgallou/dummy-qmd/tree/main/citations)
```
---
format: pdf
bibliography: refs/references.bib
csl: refs/science-without-titles.csl
# csl: refs/global-ecology-and-biogeography.csl
# csl: refs/pnas.csl
# csl: refs/nature.csl
---
@foo1999 says blah
```
Output visible [here](https://github.com/arnaudgallou/dummy-qmd/blob/main/citations/intext-science_style.pdf).
I would expect `Foo (1) says blah`.
Tested in RStudio 4.2.0 with Quarto v. 0.9.624 on macOS 12.3.1
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-06-30T15:12:53Z",
"creator": "arnaudgallou",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1259,
"state": "closed",
"title": "In-text citation formatted as `@knuth1984 says blah.` not working for citation style referencing citations form 1 to n.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1259"
} |
### Bug description
Apparently, `r-fit-text` takes into account the LaTeX "source" characters instead of the displayed ones when calculating the size of the text.
I am running quarto in preview mode, which might have to do with this issue.
The following example illustrates the problem:
```md
---
format:
revealjs:
center: true
---
## Title
::: {.r-fit-text}
r-fit-text and LaTeX don't play well with each other: $\mathcal{N}(\mathcal{a},\mathcal{b},\mathcal{c})$
:::
::: {.r-fit-text}
r-fit-text and LaTeX don't play well with each other: N(a,b,c)
:::
```
Output:
Edit: I just noticed that if the slide in question is not being currently displayed in the browser (e.g. another slide or tab is being displayed) then the line with LaTeX output is displayed correctly. This makes me think that there might be a race condition related to the time MathJax takes to render the LaTeX equations.
### System info
quarto-cli git version: `d7a4cf1cc`
```
β― quarto check
[β] Checking Quarto installation......OK
Version: 99.9.9
Path: /home/mroavi/repos/quarto-cli/package/dist/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.4
Path: /usr/bin/python3
Jupyter: 4.10.0
Kernels: julia-1.5, julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
I'm not using RStudio IDE.
My system:
```
OS: Manjaro Linux x86_64
Host: XPS 13 9360
Kernel: 5.15.36-1-rt41-MANJARO
```
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-06-30T14:35:08Z",
"creator": "mroavi",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1258,
"state": "open",
"title": "reveal.js: r-fit-text and LaTeX don't play well with each other",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1258"
} |
Perhaps I am missing something, but I am unable to include an icon with text in navbar items.
In a simple rmarkdown site, I can include both icons and text like this:
```yaml
- text: "Schedule"
icon: fa fa-calendar-alt
href: schedule.html
```
This looks like this when rendered
<img width="102" alt="Screen Shot 2022-06-30 at 9 20 02 AM" src="https://user-images.githubusercontent.com/9012994/176687569-c1993a86-3c97-4598-b357-6b86f2d51d1e.png">
In quarto, I can only get an icon or text to render, but not both. Is there a way to do this that I am missing, or is this not supported?
| {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-06-30T13:21:33Z",
"creator": "jhelvy",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 1323,
"state": "closed",
"title": "Include icons and text in navbar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1323"
} |
Hey Quarto developers,
I was not able to find any way to easily insert a page break for docx.
The solution proposed here: https://stackoverflow.com/questions/24672111/how-to-add-a-page-break-in-word-document-generated-by-rstudio-markdown may work but still leaves a little space at the top of the page.
Is there a way to insert page break?
Cheers!
| {
"assignee": null,
"comments": 1,
"created_at": "2022-06-30T08:35:23Z",
"creator": "stiatragul",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1326,
"state": "closed",
"title": "Request: page break for docx ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1326"
} |
### Bug description
When trying to render a document with a Graphviz code block on Windows 10 and error is produced.
This is in the latest build (0.9.629)
possibly related to [#295](https://github.com/quarto-dev/quarto-cli/issues/295#issue-1117132844)
Simple example:
``````
# a header text
some text
```{dot}
digraph { a -> b }
```
``````
Renders fine on Mac, but on Windows returns:
```
ERROR: TypeError: Unsupported scheme "c" for module "c:\<snip>\AppData\Local\Programs\Quarto\share\js\graphviz-wasm.js". Supported schemes: [
"data",
"blob",
"file",
"http",
"https",
]
```
quarto check:
```
[>] Checking Quarto installation......OK
Version: 0.9.629
Path: C:\<snip>\AppData\Local\Programs\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.5
Path: C:/<snip>/AppData/Local/Programs/Python/Python310/python.exe
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with py -m pip install jupyter
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/PROGRA~1/R/R-42~1.0
LibPaths:
- C:/<snip>/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.0/library
rmarkdown: 2.14
[>] 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-06-30T05:05:20Z",
"creator": "dan-cloney",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1255,
"state": "closed",
"title": "TypeError: Unsupported scheme when using Graphviz on Windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1255"
} |
### Bug description
Great tool, which I'm enjoying a lot!
Using revealjs presentation I have a pattern like this:
````md
## Slide before
Words
## The slide with the code
```{python}
#| echo: true
#| output-location: slide
# code that generates an image
```
## The slide after
Words
````
This causes the image generated by the code in the middle slide not to appear until _after_ the slide after. A bit of experimentation seems to show that the image doesn't appear until before the next slide at the top `# Single hash` level. In other words, the code-generated image doesn't show up until the end of that section of the presentation.
That is the output from the code block isn't 'flushed out' until before the next slide at a 'level above'. The behaviour is a bit reminiscent of how LaTeX flushes a 'float' image to the end of a chapter or article if it can't find a place for it.
I'm using vertical navigation, with slide-level at the default level 2. But changing those settings doesn't make any difference. The only thing that does is starting a new top-level slide.
In case it matters the code generating the image uses matplotlib plotting.
Here's the `quarto check` output
```
[β] Checking Quarto installation......OK
Version: 0.9.600
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.8 (Conda)
Path: /home/osullid3/anaconda3/bin/python
Jupyter: 4.10.0
Kernels: python3
(|) Checking Jupyter engine render....Traceback (most recent call last):
File "/opt/quarto/share/jupyter/jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "/opt/quarto/share/jupyter/notebook.py", line 17, in <module>
from nbclient import NotebookClient
ModuleNotFoundError: No module named 'nbclient'
[β] Checking Jupyter engine render....OK
```
I had not noticed the reported jupyter engine problem before this and it hasn't affected me making slides so far.
I am running VSCode 1.67.0 and the Quarto extension 1.24.0 on Ubuntu 20.0.4
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [x] 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": "cderv",
"comments": 4,
"created_at": "2022-06-30T02:54:19Z",
"creator": "DOSull",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1254,
"state": "closed",
"title": "unexpected output-location: slide behaviour in revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1254"
} |
### Bug description
Tested with Quarto 0.9.629 (inside RStudio 2022.10.0 Build 9) and 0.9.607 (outside RStudio).
Using an `index.qmd` as a non-project Quarto document:
````markdown
---
title: non-project document with variables
---
Apple cider donuts are {{< var reaction >}}.
````
This document expects values set in the `_variables.yml`:
```yaml
reaction: awesome
```
When rendering, we get a warning about the unknown variable:
```
quarto render index.qmd
# ...
# => WARNING: Unknown var reaction specified in a var shortcode.
```
The rendered HTML has the variable reference replaced by `?var:reaction`.
Creating an empty `_quarto.yml` is enough to cause this document to be processed as part of a project, and lets the variable get resolved.
```bash
touch _quarto.yml
```
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": 2,
"created_at": "2022-06-29T20:45:53Z",
"creator": "aronatkins",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1252,
"state": "closed",
"title": "variables only available in projects",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1252"
} |
### Bug description
When rendering to HTML, If I include a CSS file using `css: path/to/mycustom.css` in the header YAML, if this CSS file is referenced using a absolute path, it will not be found when running `quarto preview`.
I'm not sure if this is intended or not, but it means that the previewed version in the browser will not look the same as the rendered html (since the rendered html file can of course reference CSS files outside the local directory like `<link rel="stylesheet" href="/absolute/path/to/mycustom.css" />`). This matters if the CSS file is not inside the directory where the .(q)md file is.
At first I thought perhaps this is intentional, because the quarto preview function is meant to not reference external css files? However perhaps not, because it does let you reference external template files just fine with `template: /absolute/path/to/template`.
---
As a concrete mwe, suppose you have a file in some local location like `/Users/Shared/mycustom.css`, with some defines some CSS:
```css
body {
color: white;
background-color: black;
}
```
And suppose you have a quarto file `/Users/Shared/mytest/test.qmd`
```qmd
---
title: Title
theme: none
css: /Users/Shared/mycustom.css
---
Example body text here.
```
If you run `quarto preview /Users/Shared/mytest/test.qmd`, the output will say `/Users/Shared/mycustom.css (404: Not Found)` you'll get a preview that doesn't use the referenced CSS, even though the output HTML file is fine, and contains `<link rel="stylesheet" href=" /Users/Shared/mycustom.css" />` in the header, so it will look fine if opened in a browser, rather than through previewing.
_version info: Quarto v0.9 Build 629, macOS v12.3.1 (21E258)_
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-06-29T17:55:24Z",
"creator": "postylem",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1251,
"state": "closed",
"title": "CSS with full path not found during `preview`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1251"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1243
<div type='discussions-op-text'>
<sup>Originally posted by **ihnorton** June 29, 2022</sup>
Is it possible to target a repo other than the `origin` with `quarto publish gh-pages`? I read through the [template](https://github.com/quarto-dev/quarto-cli/blob/046f7fc0228e4480b4d9af57f92b5538f8a27e5b/src/publish/gh-pages/gh-pages.ts) and it appears not, _unless_ I misunderstood something about the handling of `siteUrl`. If not, please consider this a feature request π Thanks!</div> | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-06-29T17:24:11Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1249,
"state": "open",
"title": "Publish gh-pages to non-origin repo?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1249"
} |
When writing complicated extensions, it would be useful to specify
```
template-partials:
# Add here the partials your format is using
- "partials/*.tex"
```
instead of having to add all of them individually. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-06-29T16:46:16Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1248,
"state": "closed",
"title": "format template-partials should support globs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1248"
} |
Would it be possible to support "pauses" in revealjs presentations in slides that have multiple columns? I would like to show first one column, and after a click, the other.
E.g. the following does not work:
```md
---
format:
revealjs:
center: true
---
## The ASIA network {.smaller}
:::: {.columns}
::: {.column width="60%"}
| **Random variable** | **Meaning** |
| :---: | :--- |
| ``A`` | Recent trip to Asia |
| ``T`` | Patient has tuberculosis |
| ``S`` | Patient is a smoker |
| ``L`` | Patient has lung cancer |
| ``B`` | Patient has bronchitis |
| ``E`` | Patient has ``T`` and/or ``L`` |
| ``X`` | Chest X-Ray is positive |
| ``D`` | Patient has dyspnoea |
:::
. . .
::: {.column width="40%"}
- This is a sentence.
- This is a sentence.
- This is a sentence.
- This is a sentence.
:::
::::
``` | {
"assignee": null,
"comments": 2,
"created_at": "2022-06-29T16:23:00Z",
"creator": "mroavi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1247,
"state": "open",
"title": "Feature request: support pauses in revealjs presentations in slides with multiple columns",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1247"
} |
### Bug description
Quarto docs specify to set `output-dir: docs` for gh-pages: https://quarto.org/docs/websites/publishing-websites.html#github-pages -- and set `docs/` as the target directory in the Github Pages config.
However, running `quarto publish gh-pages` appears to ignore the `output-dir` setting.
- input: https://github.com/ihnorton/quarto-demo
- `gh-pages` after running `quarto publish gh-pages` locally (successfully): https://github.com/ihnorton/quarto-demo/tree/gh-pages
This means I need to set the Github Pages config to use `<root>` instead of `docs/`.
Running `quarto render` locally puts the output in `docs/` as expected.
---
- macOS 12.4
- quarto version:
```
base β― quarto check
```
<details>
```
[β] Checking Quarto installation......OK
Version: 0.9.629
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.13 (Conda)
Path: /Users/inorton/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: 4.1.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/inorton/Library/R/x86_64/4.1/library
- /Library/Frameworks/R.framework/Versions/4.1/Resources/library
rmarkdown: 2.9
[β] Checking Knitr engine render......OK
```
</details>
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-06-29T15:51:57Z",
"creator": "ihnorton",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0 Chores",
"number": 1246,
"state": "closed",
"title": "'quarto publish gh-pages' does not respect output-dir",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1246"
} |
### Bug description
I have a quarto website at https://github.com/jamespeapen/journals and I was building locally on Ubuntu 22.04 with quarto `0.9.489` without issues.
The last github workflow used `0.9.629` and failed with a number of errors like this:
```
ERROR: Project _quarto.yml validation failed.
In file _quarto.yml
(line 21, column 9 through line 23, column 132) Array entry 1 with value part: "Databases"
chapters:
- src/bioinformatics/databases/evaluation_of_relational_and_nosql_database_architectures_to_manage_genomic_annotations.md failed to be a string.
- 20: chapters:
- 21: - part: "Databases"
- ~~~~~~~~~~~~~~~~~
- 22: chapters:
- ~~~~~~~~~~~~~~~~~~
- 23: - src/bioinformatics/databases/evaluation_of_relational_and_nosql_database_architectures_to_manage_genomic_annotations.md
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- 24: - part: "Epigenetics"
- The value part: "Databases"
- chapters:
- - src/bioinformatics/databases/evaluation_of_relational_and_nosql_database_architectures_to_manage_genomic_annotations.md is object.
- The error happened in location book:chapters:1:chapters:0.
```
Doing a bisect, I found that the last working tag was `0.9.497` - the errors started with `0.9.498`.
I am able to reproduce this with this example:
`_quarto.yml`
```yaml
project:
type: book
book:
title: "test"
chapters:
- index.qmd
- part: "one"
chapters:
- one.qmd
- part: "two"
chapters:
- two.qmd
```
`index.qmd`, `one.qmd` and `two.qmd` are empty files in the project root.
Running `quarto render --to html` with `0.9.497` runs without error. With `0.9.498` I get:
```
ERROR: Project _quarto.yml validation failed.
In file _quarto.yml
(line 11, column 11 through line 13, column 21) Array entry 2 with value part: "two"
chapters:
- two.qmd failed to be a string.
- 10: - one.qmd
- 11: - part: "two"
- ~~~~~~~~~~~
- 12: chapters:
- ~~~~~~~~~~~~~~~~~~~
- 13: - two.qmd
- ~~~~~~~~~~~~~~~~~~~~
- The value part: "two"
- chapters:
- - two.qmd is object.
- The error happened in location book:chapters:1:chapters:1.
```
It renders only if part "two" is moved from subchapter to chapter:
```yaml
project:
type: book
book:
title: "test"
chapters:
- index.qmd
- part: "one"
chapters:
- one.qmd
- part: "two"
chapters:
- two.qmd
```
Thanks!
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": "2022-06-29T15:45:10Z",
"creator": "jamespeapen",
"is_pull_request": false,
"labels": [
"bug",
"invalid"
],
"locked": false,
"milestone": "1.0",
"number": 1245,
"state": "closed",
"title": "YAML validation failing with 0.9.498 for sub-chapters",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1245"
} |
### System info
quarto-cli git version: `d7a4cf1cc`
```
β― quarto check
[β] Checking Quarto installation......OK
Version: 99.9.9
Path: /home/mroavi/repos/quarto-cli/package/dist/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.4
Path: /usr/bin/python3
Jupyter: 4.10.0
Kernels: julia-1.5, julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
I'm not using RStudio IDE.
My system:
```
OS: Manjaro Linux x86_64
Host: XPS 13 9360
Kernel: 5.15.36-1-rt41-MANJARO
```
### Bug description
The `height` parameter does not seem to be working as expected when using absolute positioning of images. For example, the following code generates two slides with images of the same size.
```md
---
format:
revealjs:
incremental: false
---
# Test
{.absolute top=200 left=500 height="500"}
# Test
{.absolute top=200 left=500 height="1000"}
```
Here are the properties of the image I'm using:
Here is the image itself (not sure if GitHub compresses it):
Apparently, the image stops being resized if the height value is above a certain threshold. Moreover, Changing the `width` parameter has different behavior than changing the `height`. I also noticed that the image automatically appears way smaller than when using something like `{width=60% fig-align="center"}`.
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "cderv",
"comments": 1,
"created_at": "2022-06-29T15:44:22Z",
"creator": "mroavi",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1244,
"state": "open",
"title": "Aboslute positioning of images not working as expected",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1244"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1226
<div type='discussions-op-text'>
<sup>Originally posted by **sciwonder** June 26, 2022</sup>
Love the look and feel of Quatro! I was just wondering, for blogs, is it currently possible to customise the date element so that it includes date *and time* of publication? Is there a "last updated" element as well? I can imagine some circumstances where displaying the original publication date/time and the "last updated" date/time close together could be useful.</div> | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-06-29T11:22:06Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 1241,
"state": "closed",
"title": "Add Date Modified (optional) to Title Block",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1241"
} |
I tried to use Quarto to do data preprocessing in R and then make the created data available in OJS using RStudio, but it seems to me that the ojs_define function is not available. This [article ](https://quarto.org/docs/interactive/ojs/data-sources.html#python-and-r) suggests that it might be possible, but it does not seem to be working for me.
```
{r}
#| output: false
ojs_define(mtcars = mtcars)
```
In addition, it seems that using ojs from RStudio does not seem to be possible either. For example, following results in an error:
```
{ojs}
viewof bill_length_min = Inputs.range(
[32, 50],
{value: 35, step: 1, label: "Bill length (min):"}
)
```
Is there a way to do what I tried above or will it be possible eventually? | {
"assignee": "cscheid",
"comments": 21,
"created_at": "2022-06-29T10:30:20Z",
"creator": "novotny1akub",
"is_pull_request": false,
"labels": [
"enhancement",
"ojs-engine"
],
"locked": false,
"milestone": "Future",
"number": 1242,
"state": "open",
"title": "Quarto R ojs_define function and OJS in RStudio",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1242"
} |
Would it be possible to add an option to change the date title when using `title-block-style: plain`? I'd usually prefer "DATE" or "CREATED" instead of "PUBLISHED". There is already an `abstract-title:` option that allow changing the abstract title. Could a `date-title:` option be added, too?
| {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-06-29T10:29:40Z",
"creator": "fschaffner",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "1.0 Chores",
"number": 1240,
"state": "closed",
"title": "Feature request: Add \"date-title:\" option in YAML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1240"
} |
The current autostretch logic targets stand-alone images created with `{.absolute}`, such that the `width` property specified inside the `{ ... }` is ignored/overriden. This was surprising to me because I expected total control of the image when using `{.absolute}`, including its width. Setting the `height` property works, [as expected](https://github.com/cderv/quarto-cli/blob/1f2c6d4d1707a4b824af672d29faef1f797a57bc/src/format/reveal/format-reveal.ts#L679-L681), but it took a while to understand this distinction.
My thought is that absolute positioning violates the assumptions that make autostretch a good idea, beacuse repositioning an image changes what it means for the image to "stretch to fill up the slide". I don't think adding this exception will be unexpected or difficult to grok for users - it can be part of what you sign up for when you decide to `{.absolute}` an image.
Happy to work on a PR if this makes sense!
Reprex:
```
---
title: "r-stretch-reprex"
format: revealjs
---
## One `absolute` img, width set (autostretch)
{.absolute width=500}
## One `absolute` img, height set (no autostretch)
{.absolute height=100}
## Two `absolute` imgs, width set (no autostretch)
{.absolute width=500}
{.absolute top=50% width=300}
``` | {
"assignee": null,
"comments": 2,
"created_at": "2022-06-29T05:40:03Z",
"creator": "yjunechoe",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1238,
"state": "closed",
"title": "[Feature Request] Exclude {.absolute} images from autostretch",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1238"
} |
### Bug description
Using Quarto 0.9.607 (contained in a recent RStudio build -- 2022.10.0 Build 9), but have also tested Quarto 0.9.629. The same rendered results occur with both versions, and within and outside the RStudio IDE.
Observed on macOS Monterey - 12.4
Given `index.qmd` defined as:
````markdown
---
title: embedding code using includes
---
## in a code block
The `cats.R` file should be injected into the R code block and correctly
formatted without being executed.
```r
{{< include cats.R >}}
```
## outside a code block
Here is an example showing how the R code can be injected, but it does not
have the desired code-block styling.
{{< include cats.R >}}
## expected
This is the expected result when formatted:
```r
cat("cats!\n")
```
````
and a `cats.R` file defined as:
````r
cat("cats!\n")
````
The rendering should present the code from `cats.R` as formatted R code in the first code block (containing the `include`).
Instead, the rendered result has an empty code block and looks like:
<img width="524" alt="image" src="https://user-images.githubusercontent.com/362187/176269146-a06845a6-5c58-4d87-8477-f5d74cf95562.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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-06-28T19:34:00Z",
"creator": "aronatkins",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 1237,
"state": "open",
"title": "include does not inject code into a non-executable block",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1237"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1228
<div type='discussions-op-text'>
<sup>Originally posted by **ggous** June 27, 2022</sup>
Hi,
If I use highlight style:
```
format:
html:
theme: cosmo
pdf:
include-before-body:
- colors.tex
documentclass: scrreprt
code-block-bg: true
code-block-border-left: "#E9E9E9"
keep-tex: true
highlight-style: tango
```
and use double brackets for python code that I don't want to run:
`{{python}}`
then the highlight style doesn't work.
Is there any workaround for this?
</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-06-28T17:37:46Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1236,
"state": "open",
"title": "when using double brackets for code , highlight doesn't work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1236"
} |
### Bug description
Using a `{.callout}` div with a headline and footnote in HTML results in the expected output of a callout block without an icon,
the provided headline and a footnote at the end of the document.
Rendering the same example to PDF via Latex results in unexpected output (see images).
Minimal example:
```markdown
---
format: pdf
---
# Document Title
Text with a footnote^[saying nothing at all.].
::: {.callout}
## Not visible in PDF output
Some text without a footnote.
:::
::: {.callout}
## Still not visible in PDF output
A footnote^[which is inside the callout instead of outside.].
:::
```
On Pop!_OS 22.04 LTS `5.17.5-76051705-generic #202204271406~1653440576~22.04~6277a18`
Quarto check output
```
[β] Checking Quarto installation......OK
Version: 0.9.628
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: 4.10.0
Kernels: java, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.1.2
Path: /usr/lib/R
LibPaths:
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": "2022-06-28T11:36:30Z",
"creator": "fitzchivalrik",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 1235,
"state": "closed",
"title": "PDF: `{.callout}` div with heading and footnote different from HTML output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1235"
} |
I'm creating a presentation with Quarto ( to revealjs) and wanted to have one slide with a line of text centered horizontally and vertically. I could not find a way to do this. I figured that I can use the `.r-stack` to center text horizontally like
```
##
:::{.r-stack}
centered text ^[with a footnote for extra fun]
:::
```
But how can one center the line of text also vertically?
| {
"assignee": "cscheid",
"comments": 13,
"created_at": "2022-06-27T17:15:38Z",
"creator": "asmaier",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1231,
"state": "open",
"title": "How to center text in Quarto presentations?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1231"
} |
### Bug description
When a figure generated by a code block appears inside a callout, and the code block has a label starting with `fig-`, and `echo: false`, the latex compiler returns the error:
`LaTeX Error: Not in outer par mode.`
A minimal `qmd` document demonstrating this behavior is below. I am working on Ubuntu Linux with the development version of quarto installed from github.
````md
---
format: pdf
---
::: {.callout-info}
## Callout figure compiles with `echo: false` and non `fig-` label
```{r}
#| label: test
#| echo: false
plot(rnorm(100), rnorm(100))
```
:::
::: {.callout-info}
## Figure also compiles with `fig-` label but without `echo: false`
```{r}
#| label: fig-test
plot(rnorm(100), rnorm(100))
```
:::
::: {.callout-info}
## But when the two are combined, it doesn't compile
```{r}
#| label: fig-combined
#| echo: false
plot(rnorm(100), rnorm(100))
```
:::
````
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": 2,
"created_at": "2022-06-27T16:20:13Z",
"creator": "dalejbarr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 1230,
"state": "open",
"title": "latex fails to compile figure from code block when `echo: false` and `label: fig-...`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1230"
} |
Sometimes (especially with margin layout), it is useful to place the outputs of a code chunk side by side. To accomplish this, the outputs needs to come from the same chunk (e.g. a table of data and a plot of that data). It would be nice to be able to specify the labels for a chunk as an array, allowing something like:
`````
```{r}
#| label: [tbl-cars, fig-cars]
#| fig-cap: "Cars fig"
#| tbl-cap" "Cars tbl"
#| tbl-column: margin
mtcars2 <- mtcars
mtcars2$am <- factor(
mtcars$am, labels = c('automatic', 'manual')
)
knitr::kable(
mtcars[1:6, 1:6]
)
library(ggplot2)
ggplot(mtcars2, aes(hp, mpg, color = am)) +
geom_point() + geom_smooth(formula = y ~ x, method = "loess") +
theme(legend.position = 'bottom')
```
`````
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1201
<div type='discussions-op-text'>
<sup>Originally posted by **mvwestendorp** June 22, 2022</sup>
Is it possible to switch the figure and table in this [example](https://quarto.org/docs/authoring/article-layout.html#multiple-outputs)? That is, the table in the margin and figure in the body.
Using `#| tbl-column: margin` does not seem to work in this case.</div> | {
"assignee": null,
"comments": 0,
"created_at": "2022-06-27T13:29:08Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1229,
"state": "open",
"title": "Allow Different Types of Cross Reference-able Outputs from a Single Code Chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1229"
} |
Hi,
Please, I am running a quarto file with python chunks. However, when I render the document, I got an error below.
```bash
Starting python3 kernel...Done
Executing 'pytorch_tensor.ipynb'
Cell 1/82...2022-06-26 21:44:59,876 - traitlets - ERROR - Kernel died while waiting for execute reply.
Kernel died
```
<img width="1057" alt="image" src="https://user-images.githubusercontent.com/38854463/175833394-89031393-08d4-457d-981b-797742b650bd.png">
Best,
Shamsuddeen | {
"assignee": null,
"comments": 3,
"created_at": "2022-06-26T20:53:31Z",
"creator": "shmuhammadd",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1327,
"state": "closed",
"title": "Error Running .qmd file with Python chuncks",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1327"
} |
### Bug description
Hi, thanks for the great package!
When hovering over tabs (`{.panel-tabset}`), the cursor is not a pointer. See the MRE below:
````
---
title: "Untitled"
format: html
---
::: {.panel-tabset}
## Tab1
Tab 1 text
## Tab2
Tab 2 text
:::
````
Using a Bootstrap theme (e.g., `theme: cerulean`) doesn't change this behavior. I think that this is a bug, as the cursor is a pointer for tabs in R Markdown, the [Quarto documentation](https://quarto.org/docs/interactive/layout.html#tabset-panel), the [Tabby documentation/demo](https://codepen.io/cferdinandi/pen/rRMJwK), etc.
I believe that this could be fixed with some simple CSS such as `.nav-item {cursor: pointer;}`, but that might break something else, I don't know.
Many thanks!
<details>
<summary>System details</summary>
Quarto 0.9.622; R 4.2.0; RStudio 2022.02.3 Build 492; Tested on Firefox and Chrome; Pop!_OS 20.04.
</details>
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": 2,
"created_at": "2022-06-26T20:46:29Z",
"creator": "arcruz0",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1227,
"state": "closed",
"title": "Mouse cursor on tabs (`{.panel-tabset}`) is not a pointer",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1227"
} |
Maybe another option that could be added -- if the GitHub repository is public -- is opening the generated file source on a managed service like RStudio Cloud, Google Colab, Amazon Sagemaker, ...
Potentially, some kind of "click-to-share" component that houses different options? c.f.
<img width="194" alt="Screen Shot 2022-06-25 at 6 36 40 PM" src="https://user-images.githubusercontent.com/833642/175795761-096730ec-c136-4047-8bda-007c8f9e0c69.png">
| {
"assignee": null,
"comments": 1,
"created_at": "2022-06-26T01:39:52Z",
"creator": "coatless",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1224,
"state": "open",
"title": "[feature-request] Open notebook/chapter in [rscloud, colab, sagemaker, watson studio, azure notebooks, ...]",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1224"
} |
### Bug description
# Problem
I'm trying to customize the category labels in blog posts and on the listings page via a custom theme. This theme is defined via a file `theme.scss` and contains the following content:
```
/*-- scss:defaults --*/
$primary: #06436e !default;
$white: #fff !default;
/*-- scss:rules --*/
// This works and changes the tag appearance on the listing page
div.quarto-post .listing-categories .listing-category {
background-color: $primary;
color: $white;
font-size: 14px;
font-weight: 600;
text-transform: none;
border-radius: 0.25cm;
}
// This does not work: The output contains a opacity less than 1.
.quarto-title .quarto-categories .quarto-category {
opacity: 1;
color: $white;
background-color: $primary;
}
```
The first rule works nicely and the tag labels on the listing pages change. However, the second rule does not work and the tags are not displayed properly in the blog posts. This is because in the rendered file `bootstrap.min.css`, I can find both my code and a few lines further down
```
.quarto-title .quarto-categories .quarto-category {
padding:.25em .75em;
font-size:.65em;
text-transform:uppercase;
border:solid 1px;
border-radius:.25rem;
opacity:.6
}
```
I suspect that this is some default bootstrap setting and these overwrite the changes that I want to make. A workaround is to create an additional CSS file and include it in the blog via `_quarto.yml`.
Related problem: My initial workaround was to include the CSS file in each blog post with `include-in-header` in `posts/_metadata.yml`. Unfortunately, this incorporated the CSS file as text into the blog post instead of into the header.
# Reprex
Can be found at https://github.com/AlbertRapp/bootstrap_quarto_blog
# System Information
```
[β] Checking Quarto installation......OK
Version: 0.9.385
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: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.0
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
RStudio
2022.02.3 Build 492
Β© 2009-2022 RStudio, PBC
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
```
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2022-06-25T14:22:58Z",
"creator": "AlbertRapp",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1223,
"state": "closed",
"title": "Bootstrap changes get overwritten in blog posts",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1223"
} |
### Bug description
Figure captions over a certain length cause consistent rendering failures. Here is a minimal example:
```
---
title: "matplotlib demo"
format:
html:
code-fold: true
jupyter: python3
---
For a demonstration of a line plot on a polar axis, see @fig-polar.
```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis A line plot on a polar axis A line plot on a polar axis"
import numpy as np
import matplotlib.pyplot as plt
r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
subplot_kw = {'projection': 'polar'}
)
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```
Rendering using `quarto render test.qmd` gives:
```
Starting python3 kernel...Done
Executing 'test.ipynb'
Cell 1/1...ERROR:
None of the known patterns match for axis
```
I believe this may also relate to https://github.com/quarto-dev/quarto-cli/issues/1194.
---
# System info
```
:: quarto check
[β] Checking Quarto installation......OK
Version: 0.9.619
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.5
Path: /home/cjber/qtest/.direnv/python-3.10.5/bin/python3
Jupyter: 4.10.0
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib64/R
LibPaths:
- /home/cjber/.r
- /usr/lib/R/library
rmarkdown: 2.14.3
[β] Checking Knitr engine render......OK
```
Running Arch Linux:
```
:: uname -r
5.18.6-arch1-1
```
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-06-25T14:12:34Z",
"creator": "cjber",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1222,
"state": "closed",
"title": "Long figure captions cause render failure 'None of the known patterns match for ...'",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1222"
} |
I've got R v4.2.0 and Quarto downloaded this week. When I run quarto check in the Windows command prompt, I get an error that regdmp cannot fetch the hkey_local_machine... relevant to the R installation. I can open regedit and see that the desired path regdmp is looking for is there, and that it contains the right install path for R, but the "access denied" message is stopping me in my tracks. What shoudl I try next? | {
"assignee": null,
"comments": 26,
"created_at": "2022-06-25T05:45:32Z",
"creator": "ajrgodfrey",
"is_pull_request": false,
"labels": [
"windows"
],
"locked": false,
"milestone": "Future",
"number": 1225,
"state": "open",
"title": "regdmp has access denied",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1225"
} |
### Bug description
I am switching between `knitr` and `jupyter` engines for rendering a Matplotlib figure using the following reprex:
````
---
engine: jupyter # knitr
---
```{python}
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(0, 2 * np.pi, 100) # 100 values from 0 to 2π
fig, ax = plt.subplots()
ax.plot(x, np.sin(x))
ax.set_title("jupyter") # knitr
fig.patch.set_facecolor("red")
plt.show()
```
````
I noticed that the figure in the rendered HTML looks different depending on the engine.
knitr:
jupyter:
I would expect that figures look identical independent of the rendering engine. Regardless of whether or not this is a bug, is there a workaround that sets a specified figure resolution/DPI/scale/... (for knitr and jupyter engines)?
I tried this on macOS 11.6.7.
<details>
<summary>Output of `quarto --check`:</summary>
```
[β] Checking Quarto installation......OK
Version: 0.9.613
Path: /Users/clemens/Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.4
Path: /Users/clemens/Repositories/python_data_analysis/.venv/bin/python3
Jupyter: 4.10.0
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/Resources/library
rmarkdown: 2.13
[β] Checking Knitr engine render......OK
```
</details>
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": "2022-06-24T07:29:18Z",
"creator": "cbrnr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1219,
"state": "closed",
"title": "Rendered figure size depends on engine",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1219"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1198
<div type='discussions-op-text'>
<sup>Originally posted by **dfalbel** June 21, 2022</sup>
We have a Quarto website with a `style: "docked"` sidebar which we find too narrow for the items titles.
I have found that the following does what we want but adds extra margin to the mobile view which we don't really want.
```
/*-- scss:mixins --*/
$grid-screen-inset-padding: 1.5em;
```
I wonder what's would be the best way to modify the sidebar width.
Here's the current behavior:
And the desired:
</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-06-23T17:27:27Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 1212,
"state": "closed",
"title": "How to increase the sidebar width?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1212"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1172
<div type='discussions-op-text'>
<sup>Originally posted by **harrelfe** June 17, 2022</sup>
I specify cap-location: margin in my Quarto book yaml. For the few figures that have multiple panels this causes the figures to no longer be rendered in a matrix but rather as larger individual plots. Is there a way to override cap-location for one code chunk? Here's some test code:
---
title: "Test"
format:
html:
self-contained: true
cap-location: margin
---
```{r}
#| label: fig-test
#| fig.width: 8
#| fig.height: 8
#| fig.scap: 'Four examples of residual plots'
#| fig.cap: 'Using residuals to check some of the assumptions of the simple linear regression model.'
#| fig-subcap:
#| - "Non-constant $\\sigma^2$, which might call for transforming $y$"
#| - "Constant $\\sigma^2$ but systemic failure of the linearity assumption"
#| - "Ideal situation of white noise (no trend, constant variance)"
#| - "$q-q$ plot demonstrating approximate normality of residuals, for a sample of size $n=50$. Horizontal reference lines are at zero, which is by definition the mean of all residuals."
#| layout-ncol: 2
plot(rnorm(20)); plot(runif(20)); hist(rnorm(100)); hist(rexp(100))
```
</div> | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-06-23T17:26:23Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1211,
"state": "closed",
"title": "How to override format: html: cap-location: margin",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1211"
} |
### Bug description
<img width="1006" alt="image" src="https://user-images.githubusercontent.com/285675/175357986-28a7c787-9ba7-47ed-a79a-c43c3904392e.png">
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, self-contained, and reproducible example?
- [ ] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": "2022-06-23T17:22:27Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1210,
"state": "closed",
"title": "bad yaml validation with jupyter C engine",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1210"
} |
Hi! Thanks for making an awesome tool!!
When I use grid and I don't have an image, the image box comes up as gray. I know I can set a default image, but I don't want to do that. I'd like the grid card to just hide the image portion of the image isn't supplied.
This could be a good _index.qmd specification perhaps?
 | {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2022-06-23T17:12:22Z",
"creator": "bryanwhiting",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1213,
"state": "open",
"title": "Hide image display if not in front matter on grid display",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1213"
} |
### Bug description
In the latest version of quarto,when I compile the documentation using Lua scripts as a filter, I get the following error.This is a very important filter in scientific writing (Better Bibtex) that helps us to change plain text literature into literature in Word. You can view this filter below(https://retorque.re/zotero-better-bibtex/exporting/zotero.lua). I don't know if it was a problem with the filter or with quarto, but the problem was solved when I went back to version 0.9.551.
```lua
zotero-live-citations f34bfc770
Error running filter /Users/XXX/zotero.lua:
/Users/XXX/zotero.lua:1891: attempt to call a nil value (field 'next_id')
stack traceback:
```
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [X] 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": 3,
"created_at": "2022-06-23T15:04:00Z",
"creator": "williamlorder",
"is_pull_request": false,
"labels": [
"bug",
"verify-fixed"
],
"locked": false,
"milestone": "1.0",
"number": 1206,
"state": "closed",
"title": "A serious problem with Pandoc's lua script stopped the document from being compiled into DOCX",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1206"
} |
### Bug description
The code below fails to render with the following error on Quarto v0.9.600:
```
ERROR: TypeError: item.author.join is not a function
```
````
---
format: html
listing:
- id: table
type: table
contents:
title: "My cool report"
subtitle: "It has neat things in it"
date: "2022-06-23"
author: "Tom Mock"
---
::: {#table}
:::
````
If I remove the `author: name` key-value pair the rest of the document will render successfully.
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": 6,
"created_at": "2022-06-23T14:57:41Z",
"creator": "jthomasmock",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "1.0",
"number": 1205,
"state": "closed",
"title": "Manually generating listing with author results in error.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1205"
} |
### Bug description
Trying to generate a listing or custom listing in formats other than a Quarto project: website silently fail and doesn't do anything.
It would be great to be able to leverage listings outside of websites to generate tables, cards, grids, etc for single-page applications/reports without having to use R/Python. If it's not reasonable to add this feature to non-websites, it would be good to error/warn the user that it's not doing anything.
Minimal example - works on a website, but fails silently without the `_quarto.yml` file using Quarto: 0.9.600
````
---
format: html
listing:
- id: table
type: table
contents:
title: "My cool report"
subtitle: "It has neat things in it"
date: "2022-06-23"
---
::: {#table}
:::
````
### 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, self-contained, and reproducible example?
- [X] documented the quarto version you're running, by providing the output produced by `quarto check` in a terminal in your issue?
- [ ] 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": "cscheid",
"comments": 0,
"created_at": "2022-06-23T14:54:44Z",
"creator": "jthomasmock",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1204,
"state": "open",
"title": "Provide error or feature for listings outside of websites",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1204"
} |
Hi,
I noticed that `ojs_define` is only defined using Python and R, but not Julia.
Is there any particular reason why this is the case?
I coded a quick implementation of it myself and so far it seems to be working fine.
Here is a MWE notebook code:
````
---
title: ojs_define using Julia
---
```{julia}
using JSON3, DataFrames, JSONTables
convert(x) = x
convert(x::AbstractDataFrame) = JSONTables.ArrayTable(Tables.rows(x))
function ojs_define(; kwargs...)
content = Dict("contents" => [Dict("name" => k, "value" => convert(v)) for (k, v) in kwargs])
tag = "<script type='ojs-define'>$(JSON3.write(content))</script>"
IJulia.display(MIME("text/html"), tag)
end
ojs_define(
array=[1,2,3],
string="somestring",
dict=Dict("a" => 1, "b" => [1, 2]),
df=DataFrame(x=randn(100), y=randn(100))
)
```
```{ojs}
array
string
dict
df
Plot.plot({
grid: true,
marks: [
Plot.dot(df, { x: "x", y: "y" })
]
})
```
````
I am not familiar with the internals of quarto, but if you think this feature is worth implementing I am glad to open a pull request. | {
"assignee": "cscheid",
"comments": 9,
"created_at": "2022-06-23T11:07:57Z",
"creator": "p-gw",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1203,
"state": "closed",
"title": "`ojs_define` in Julia",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1203"
} |
As discussed at the Boston R Users meeting tonight, it would be nice to see quarto gracefully handle setting page breaks in HTML documents. Use case:
- Prepare a well-designed HTML report that can be sent via email and open/read by non-technical users
- Deliver report to users who will:
- view in browser of choice, and/or
- print a copy, expecting clean page breaks like in a docx file.
Basically, smart CSS print style sheets by default, or with ease. | {
"assignee": null,
"comments": 2,
"created_at": "2022-06-22T01:54:33Z",
"creator": "orderlyquant",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1200,
"state": "open",
"title": "Feature request: Page Breaks for printing HTML output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1200"
} |
If I create a figure or table in raw latex:
```latex
\begin{figure}[h!]
\begin{center}
\includegraphics[width=\textwidth]{figure/path}
\end{center}
\caption{My caption}
\label{fig-label}
\caption*{\footnotesize Note: A note}
\end{figure}
```
I can't cross-reference `@fig-label`. Is that by design? Is there some way to have them be cross-references as a workaround?
The reason I need to use raw latex instead of using markdown, is that I need a note underneath the figure. If there's some way to do that with using markdown, that would be even better! | {
"assignee": null,
"comments": 6,
"created_at": "2022-06-21T21:19:03Z",
"creator": "amichuda",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1199,
"state": "open",
"title": "cross-reference labels from raw latex",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1199"
} |
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