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stringlengths 0
46.9k
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|---|---|
It would be great if the math preview was aware of user-defined macros, the ones supported by pandoc, which are automatically expanded in processing. Otherwise, the preview is a mess. I understand that this might be a bit more of an involved change.. | {
"assignee": "jjallaire",
"comments": 4,
"created_at": "2022-10-04T08:21:49Z",
"creator": "lcnbr",
"is_pull_request": false,
"labels": [
"enhancement",
"yaml-validation",
"editors"
],
"locked": false,
"milestone": "v1.4",
"number": 2884,
"state": "open",
"title": "Macro expand math preview",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2884"
} |
### Bug description
I have organization-internal document classes that I'd like to use with Quarto. I can render to a `latex` output, and then build the PDF myself, but I'd ideally like to render `.qmd` files to PDFs all in one step.
Specifying a path to `documentclass` causes Quarto to search for the path on TeXLive if `latex-auto-install` is enabled. If `latex-auto-install` is disabled, then a corrupted PDF file is generated (the file cannot be opened).
I have a global `TEXINPUTS` variable set, which works with `latexmk`, but Quarto does not seem to use that variable.
Is there any way to specify local LaTeX packages and classes?
| {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-10-04T03:10:31Z",
"creator": "jcarpi",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2718,
"state": "closed",
"title": "Specifying Local TeX packages and classes",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2718"
} |
### Bug description
This might be better directed to @rocker-org, but I'll start here! I've endeavoured to [set up a VSCode devcontainer](https://github.com/360-info/quarto-scaffold/tree/test-container) for our Quarto projects based on the R community devcontainer template (which in turn uses the `rocker/r-ver:4.2` Docker image). Quarto is included in the image, but attempts to render a [test case](https://github.com/360-info/quarto-scaffold/blob/test-container/index.qmd) lead to a Pandoc error:
```
$ quarto render index.qmd
Killed
Error in strsplit(info, "\n")[[1]] : subscript out of bounds
Calls: .main ... pandoc_available -> find_pandoc -> lapply -> FUN -> get_pandoc_version
In addition: Warning message:
In system(paste(shQuote(path), "--version"), intern = TRUE) :
running command ''/usr/local/bin/pandoc' --version' had status 137
Execution halted
```
Even just running `pandoc --version`, using the version of Pandoc that Quarto appears to be calling, fails:
```
$ pandoc --version
Killed
```
I should say that the test case renders fine with my own local Quarto installation!
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 16,
"created_at": "2022-10-04T01:56:22Z",
"creator": "jimjam-slam",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2716,
"state": "closed",
"title": "Pandoc memory issue in amd64 docker container emulated on M1 Mac",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2716"
} |
Hello,
There is a bug.
In my quarto book file 03-tidy_data.qmd
the code block is
```r
#| label: tbl-birth
#| tbl-cap: "Birth table"
load("dataset/births.rda")
births
```
_quarto.yml settings
``` yaml
format:
html:
theme: cosmo
df-print: paged
```
@tbl-birth
when I render the book, there is a warning
> WARNING: 03-tidy_data.html: Unable to resolve crossref @tbl-birth
Watching files for changes
The crossref is available when I change the code block using `kable()`, but it's not paged
```r
#| label: tbl-birth
#| tbl-cap: "Birth table"
births <- import("dataset/births.rda")
knitr::kable(births)
```
I want both of crossref and paged available. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-10-03T14:20:09Z",
"creator": "hao203",
"is_pull_request": false,
"labels": [
"needs-repro",
"tables"
],
"locked": false,
"milestone": "v1.2",
"number": 2712,
"state": "closed",
"title": "crossref table error with paged table",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2712"
} |
I followed instructions from documentation, but it didn't work:
```_quarto.yml
project:
type: book
book:
title: "My book title"
language: "pt-BR"
chapters:
- index.qmd
format:
html:
theme: cosmo
````
_Originally posted by @fredguth in https://github.com/quarto-dev/quarto-cli/discussions/2453#discussioncomment-3779914_
| {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-10-03T08:27:53Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.3",
"number": 2707,
"state": "closed",
"title": "changing language of a book does work with `language` key",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2707"
} |
### Bug description
## Issue
In `_quarto.yml`, `resources` data after `output-dir` does not work.
Below is an example of `_quarto.yml` that does not include `test.html` in the `docs` directory.
```
project:
type: website
output-dir: docs
resources:
- "test.html"
```
This is an example that works as expected.
```
project:
type: website
resources:
- "test.html"
output-dir: docs
```
## My environment
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_5_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-10-03T00:19:11Z",
"creator": "chadyuu",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2706,
"state": "closed",
"title": "Cannot include resources",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2706"
} |
### Bug description
Hi there, first time submitting an issue, so I hope I get all the information you need.
I was trying to put some information followed by a citation in parenthesis. For example: (this is a piece of information; Bananas, 2022). So I tried to use the citation syntax: `[this is a piece of information; @Bananas2022]`. However, this preserves the square brackets and render the citation as if it were an inline citation as: [this is a piece of information; Bananas (2022)]
I tested in four examples that you can see in the code and pictures below. A reproducible (I hope) example files are at the end. This might be a Pandoc Issue rather than quarto, but I am not sure.
Using a `,` seems to work fine, but it mess the chronological order if multiple citations are included
Thanks!
```
---
title: "Notes and citations and square brackets"
# format: html
format: docx
# format: pdf
bibliography: references.bib
---
1. Unexpected output citation square brackets preserved, citation
format as in-line [e.g., bananas; @quarto]
2. Expected output in PDF, but missing `;` in word and html [e.g.,
bananas`;`{=latex} @quarto]
3. Same as example 2, but `;` also missing in pdf[e.g.,
bananas`;`{=openxlm
} @quarto]
4. Trying to trick .docx output, did not work. got double `;` in .pdf
[e.g., bananas ;`;`{=latex} @quarto]
```
# HTML output:
# Pdf output
# docx output
# Reproducible code (I hope)
I had to include two files, the .qmd and the .bib file
[Test.zip](https://github.com/quarto-dev/quarto-cli/files/9693720/Test.zip)
# Details
R version: 4.2.1
R studio version: 2022.07.0 Build 548
Quarto version: 1.1.251
windows version: 10.0 build 19044
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-10-02T23:02:20Z",
"creator": "cicarrascog",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2705,
"state": "closed",
"title": "Wrong citation format when text and citations are included inside square brackets",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2705"
} |
It seems that any aside block will shift any math content to below it: 
This seems like some bad overlap between math ax divs and aside ones | {
"assignee": "dragonstyle",
"comments": 5,
"created_at": "2022-10-02T15:43:48Z",
"creator": "lcnbr",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2701,
"state": "closed",
"title": "Asides shifts math",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2701"
} |
# Problem
Creating website projects in RStudio always fails with the following error:
If I create it locally on the C: drive and then copy it back to the network drive, I get the following error
```
ERROR: NotFound: The system cannot find the path specified. (os error 3), stat 'UNC\Thor\users\tgummer\quarto_website'
```
I don't have an in depth knowledge of how UNC paths work but according to my understanding that instead of having the "UNC\" in it, this path should be either `\\Thor\users\tgummer\quarto_website` or `H:\tgummer\quarto_website` (as `\\Thor\users` is mapped to `H:` on my computer).
This indicates to me that quarto is somehow not recognising file paths on the network drives as existing or perhaps certain generated files aren't getting created quickly enough and the process is getting stuck
# System
I used RStudio (but also tired the command line as well with the same result) on windows to render my quarto website/setup the project.
# Caveats
It is only websites that aren't working, Quarto documents are working fine.
Wesbites also render fine on the local C: drive. | {
"assignee": null,
"comments": 3,
"created_at": "2022-10-02T04:03:24Z",
"creator": "t-gummer",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2711,
"state": "closed",
"title": "Error when rendering quarto websites on mapped/network drives/UNC paths on Windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2711"
} |
(for other quarto devs: this is a side-project of mine anyway, so it's easy to make it official)
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2653
<div type='discussions-op-text'>
<sup>Originally posted by **slimhk45** September 28, 2022</sup>
There is already support for KaTeX in mathematics, it would be good as well to include support for ABC notation in music.</div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-10-02T03:11:14Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"third-party"
],
"locked": false,
"milestone": "Future",
"number": 2700,
"state": "open",
"title": "Add support for ABC notation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2700"
} |
### Bug description
The stdout of the embedded pandoc is getting redirected to stderr. For example:
```
quarto pandoc --version 2> /dev/null
```
outputs nothing (`2>` redirects stderr) but
```
pandoc --version 2> /dev/null
```
does output the version message.
This holds for other outputs of pandoc to stdout.
I am not directly affected by this, but I can imagine some piping scenarios where this could be pretty annoying.
VERSION:
```
$ quarto --version
1.1.251
$ cat /etc/os-release
NAME="Fedora Linux"
VERSION="36 (Container Image)"
ID=fedora
VERSION_ID=36
VERSION_CODENAME=""
PLATFORM_ID="platform:f36"
PRETTY_NAME="Fedora Linux 36 (Container Image)"
```
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-10-01T21:41:01Z",
"creator": "castedo",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 2699,
"state": "open",
"title": "quarto embedded pandoc stdout redirected to stderr",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2699"
} |
### Bug description
Url fields in bibtex render separately, not as hrefs on the title.
I believe the default behavior in citeproc is to have the title field from the bibtex to be the text for the link. This is not how they render on the sidebar using quarto (version 1.0.37)
Osx 11.1, m1 macbook.
<img width="1088" alt="Screen Shot 2022-10-01 at 3 57 39 PM" src="https://user-images.githubusercontent.com/43227/193426222-ba0ae528-3e3b-46c4-811a-a4380e69b8cc.png">
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2022-10-01T19:58:26Z",
"creator": "rahuldave",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2696,
"state": "closed",
"title": "url fields in bibtex render separately, not as hrefs on the title",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2696"
} |
### Bug description
Hello,
I'm trying to create an interactive HTML document using jupyter widgets. here are the python code chuck in my qmd file:
````
---
title: "Test - Embed widget"
author: byryepez
format: html
---
## Creating plotting function
```{python}
import pandas as pd
import matplotlib.pyplot as plt
from ipywidgets import widgets, interact
data = {
'x' : [1,2,3,1,2,3,1,2,3],
'y' : [1,2,3,4,5,6,7,8,9],
'p' : ['A','A','A','B','B','B','C','C','C']
}
df = pd.DataFrame(data)
def exp_plot(datasource, a):
dfset = datasource.query('p == @a')
return dfset.plot.line(x='x',y='y')
def int_plot(param_a):
return exp_plot(datasource=df, a= param_a);
interact(int_plot, param_a =['A', 'B', 'C']);
plt.show()
```
````
When I render the file to HTML, the document is not interactive, the plot is frozen to the default option. If I render the qmd file to jupyter, the document it is interactive, no issue.
I'm runing in Linux x64 5.15.65-1-MANJARO, quarto: 1.1.251, python: 3.10.6 64-bit on VSCODE 1.71.2
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-10-01T13:33:05Z",
"creator": "byryepez",
"is_pull_request": false,
"labels": [
"jupyter"
],
"locked": false,
"milestone": "v1.2",
"number": 2693,
"state": "closed",
"title": "Embed jupyter widget not working",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2693"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2690
<div type='discussions-op-text'>
<sup>Originally posted by **castedo** September 30, 2022</sup>
With the attached qmd file [license.qmd.txt](https://github.com/quarto-dev/quarto-cli/files/9688255/license.qmd.txt) I can do the following:
```
quarto pandoc license.qmd --from markdown -s --to jats 2> good.xml
```
but the following
```
quarto render license.qmd --to jats
```
fails with
```
ERROR: Validation of YAML front matter failed.
ERROR: In file license.qmd
(line 7, column 3 through line 11, column 26) Key license has value type: open-access
link: "https://creativecommons.org/licenses/by/4.0/"
...
This document is distributed under a Creative Commons Attribution 4.0
International license., which must be a string
6: license:
7: type: open-access
~~~~~~~~~~~~~~~~~
8: link: "https://creativecommons.org/licenses/by/4.0/"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
...
10: This document is distributed under a Creative Commons Attribution 4.0
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11: International license.
~~~~~~~~~~~~~~~~~~~~~~~~~
12: ---
✖ The value type: open-access
link: "https://creativecommons.org/licenses/by/4.0/"
...
This document is distributed under a Creative Commons Attribution 4.0
International license. is object.
ℹ The error happened in location license.
ERROR: Render failed due to invalid YAML.
```
That's with quarter version 1.1.251.
The documentation of pandoc described the license key while the quarto JATS ref does not list support for this license key.
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-10-01T12:56:06Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 2691,
"state": "closed",
"title": "Feature request: support JATS license like pandoc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2691"
} |
We don't want this to happen:
| {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-30T19:42:18Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2688,
"state": "closed",
"title": "support `crossref: false` in formats",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2688"
} |
This should work:
```
---
format:
customformat.lua: default
---
```
Instead we get a validation error. With `validate-yaml: false` everything works as expected. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-09-30T19:19:43Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2687,
"state": "closed",
"title": "support custom writers as format keys",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2687"
} |
## Bug description
Hello! I am using Quarto (version 0.9.531) on Windows 10 (I am running RStudio IDE version 2022.07.2+576), to output a PDF Curriculum Vitae. Everything was going great, until I decided to change the font and style of the section headers. And the logic way to do this in Latex, is by using the `titlesec` package. However, a Latex conflict is happening when I include the `titlesec` package. The resulting error produced by xelatex, when I include the `titlesec` package is this:
```
compilation failed- error
Argument of \paragraph has an extra }.
<inserted text>
\par
l.1641 \ttl@extract\paragraph
see E:\Users\pedro\Documents\curriculo\titlesec-error.log for more information.
```
I started to research a little about this error, and, by doing some tests, I discovered that the source of the Latex error/conflict happens because of this section of the Latex code that is produced by default by Pandoc/Quarto:
```tex
% Make \paragraph and \subparagraph free-standing
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi
```
In other words, if I remove this Latex code from `titlesec-error.tex`, and, try to compile the `.tex` file again with xelatex, everything works perfectly, without errors.
If I undestood correctly, looks to me that the Latex conflict is happening because `titlesec` looks for a specific definition of `\paragraph` command. However, with the latex code above, we are redefining the `\paragraph` command to a different version (I might be wrong).
## Reproducible example
If you want to reproduce this error, you can do it by using the `titlesec-error.qmd` and `pdf_config.tex` files, which are exposed below. The `titlesec-error.qmd` file is composed of these lines:
```md
---
title: "Pedro Duarte Faria"
format:
pdf:
keep-tex: true
documentclass: article
number-sections: true
colorlinks: true
geometry:
- top=2cm
- bottom=3cm
- left=2.5cm
- right=2.5cm
include-in-header:
- pdf_config.tex
fontsize: 11pt
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
```
And the `pdf_config.tex` is composed of the following lines:
```tex
\usepackage{titlesec}
\titleformat*{\section}{\Large\bfseries\fontforsection}
```
## More infos about the system and session
My `tmlgr` version is:
```r
system("tlmgr --version")
```
```
tlmgr revision 63068 (2022-04-18 07:58:07 +0200)
tlmgr using installation: C:/Users/pedro/AppData/Roaming/TinyTeX
TeX Live (https://tug.org/texlive) version 2022
```
The basic info about my session:
```r
sessionInfo()
```
```
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
Matrix products: default
locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8 LC_CTYPE=Portuguese_Brazil.utf8 LC_MONETARY=Portuguese_Brazil.utf8
[4] LC_NUMERIC=C LC_TIME=Portuguese_Brazil.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.0 tools_4.2.0 tinytex_0.38 xfun_0.30
```
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 7,
"created_at": "2022-09-30T16:47:11Z",
"creator": "pedropark99",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2686,
"state": "closed",
"title": "Latex conflict when including the `titlesec` package",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2686"
} |
### Bug description
In the example below, I highlight some lines progressively using `|` in `code-line-numbers`. However, after the first step, the "copy code" button doesn't appear anymore when I hover the code chunk.
I'm not sure which behavior is expected: hide the copy button as soon as there's some line highlighting, or enable it all the time?
````rmd
---
format: revealjs
---
```{.r code-line-numbers="1|2"}
line1
line2
```
````
---
quarto v. 1.2.171
Windows 10 x64 (build 19044)
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 1,
"created_at": "2022-09-30T16:00:18Z",
"creator": "etiennebacher",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 2685,
"state": "closed",
"title": "revealjs: highlighting lines with `|` hides the copy button after the first step",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2685"
} |
### Bug description
I tried the latest quarto cli and it opened the wrong port (6582).
The correct port seems to be the one shown on the command line (3512).
(Note that the command was executed on the terminal in the VSCode Dev Containers.)
```sh
$ quarto check
[✓] Checking Quarto installation......OK
Version: 1.2.171
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.10.6
Path: /usr/local/bin/python3
Jupyter: 4.11.1
Kernels: python3
[✓] Checking Jupyter engine render....OK
[✓] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 12,
"created_at": "2022-09-30T14:03:23Z",
"creator": "eitsupi",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2684,
"state": "closed",
"title": "Running the `quarto preview` command in a docusaurus project opens the wrong port (on VSCode)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2684"
} |
### Bug description
From https://github.com/quarto-ext/code-filename/issues/3 but extensions has been included inside core now.
````markdown
---
title: Test
format: html
---
Non computation code filename
```{.r filename="file.R"}
1 + 1
```
Inside code-fold
```{r filename="file.R"}
#| code-fold: true
1 + 1
```
````
Do we want to support `filename` on computational chunk ? (which does not follow the YAML in chunk syntax)
If not, we should deactivate.
If we do, we maybe to introduce as YAML option and/or put the filename inside the folding of source.
Related Discussion item: https://github.com/quarto-dev/quarto-cli/discussions/2642
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-09-30T12:42:30Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2683,
"state": "open",
"title": "Code filename not correctly placed when used on computational chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2683"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2678
<div type='discussions-op-text'>
<sup>Originally posted by **cbrnr** September 30, 2022</sup>
Recently, it took me longer than I'd like to admit to find out why the following code chunk gets evaluated despite setting the corresponding option:
````
---
title: Test
---
```{r}
#| eval: false
cat("Hello")
```
````
If you want to reproduce, copy this example to a file `test.qmd` and preview it with `quarto preview test.qmd`.
In fact, the cell is evaluated because I accidentally used a non-breaking space (U+00A0, <kbd>⌥</kbd><kbd>Space</kbd> on a Mac) instead of a normal space after the `#|` characters. I now turned on `"editor.unicodeHighlight.includeComments": true` and `"editor.unicodeHighlight.nonBasicASCII": true` in Visual Studio Code, which makes this obvious, but I thought that maybe Quarto could issue a warning (or info) when encountering unknown chunk options. Currently, I didn't find anything even after setting `--log-level info`. WDYT?</div> | {
"assignee": "cscheid",
"comments": 10,
"created_at": "2022-09-30T08:21:53Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2681,
"state": "closed",
"title": "chunk options with non-breaking space does not work and are not shown as invalid",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2681"
} |
### Bug description
I created a blog based on Quarto and imported about 200 old articles in markdown and Jupyter Notebooks.
It is on Github: https://github.com/zonca/zonca.dev
The problem is that when I run `quarto render`, it builds all the posts, but then hangs, with no error.
The render is actually complete, if I kill it and then publish the website, it looks fine.
I am on Debian GNU/Linux 10 (buster) on a Chromebook, the problem is that I deployed to Netlify following the documentation, and it hangs also there just after building the last post.
Not sure what I could do to understand the issue.
I tried to increase the logging level, but I only get:
```
[219/219] consult.qmd
[INFO] Loaded /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/template.patched from /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/template.patched
[INFO] Loaded /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/metadata.html from /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/metadata.html
[INFO] Loaded /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/title-block.html from /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/title-block.html
[INFO] Loaded /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/title-metadata.html from /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/title-metadata.html
[INFO] Loaded /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/toc.html from /tmp/quarto-session1ce7b4a5/989e2697/87ee8d18/toc.html
[INFO] Running filter /opt/quarto/share/filters/quarto-init/quarto-init.lua
[INFO] Completed filter /opt/quarto/share/filters/quarto-init/quarto-init.lua in 11 ms
[INFO] Running filter /opt/quarto/share/filters/authors/authors.lua
[INFO] Completed filter /opt/quarto/share/filters/authors/authors.lua in 11 ms
[INFO] Running filter /opt/quarto/share/filters/quarto-pre/quarto-pre.lua
[INFO] Completed filter /opt/quarto/share/filters/quarto-pre/quarto-pre.lua in 31 ms
[INFO] Running filter /opt/quarto/share/filters/crossref/crossref.lua
[INFO] Completed filter /opt/quarto/share/filters/crossref/crossref.lua in 14 ms
[INFO] Running filter /opt/quarto/share/filters/layout/layout.lua
[INFO] Completed filter /opt/quarto/share/filters/layout/layout.lua in 15 ms
[INFO] Running filter /opt/quarto/share/filters/quarto-post/quarto-post.lua
[INFO] Completed filter /opt/quarto/share/filters/quarto-post/quarto-post.lua in 12 ms
[INFO] Running filter /opt/quarto/share/filters/quarto-finalize/quarto-finalize.lua
[INFO] Completed filter /opt/quarto/share/filters/quarto-finalize/quarto-finalize.lua in 11 ms
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 5,
"created_at": "2022-09-30T05:13:27Z",
"creator": "zonca",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2676,
"state": "closed",
"title": "Quarto render hangs after building website",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2676"
} |
### Bug description
STEPS: from empty directory on Linux
```
sudo mkdir /tmp2
sudo mount -t tmpfs tmpfs /tmp2
echo Hi > test.qmd
touch _quarto.yml
quarto render test.qmd --to markdown --output-dir /tmp2
```
RESULT: quarto outputs:
```
ERROR: Invalid cross-device link (os error 18), rename '/home/castedo/shr/bugs/q2/test.md' -> '/tmp2/test.md'
```
NOTES:
1) This works:
```
quarto render test.qmd --to markdown --output-dir tmp2
```
2) So does
```
echo Hola > /tmp2/hi.txt
cat /tmp2/hi.txt
```
3) These steps with a tmpfs are not my actually usage scenario. I hit this because I run quarto inside a container and was outputing into a public_html directory mounted outside the container. Similar issue should get hit with VMs and shared folders.
Easy for me to work around though.
ENVIRONMENT:
```
[castedo@quarto-1 1]$ quarto --version
1.1.251
[castedo@quarto-1 1]$ cat /etc/os-release
NAME="Fedora Linux"
VERSION="36 (Container Image)"
ID=fedora
VERSION_ID=36
...
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-09-30T01:00:43Z",
"creator": "castedo",
"is_pull_request": false,
"labels": [
"bug",
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 2671,
"state": "open",
"title": "--output-dir fails on cross-device destination",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2671"
} |
### Bug description
STEPS:
Run the following in an empty directory:
```
echo Hi > test.qmd
quarto render test.qmd --to markdown --output-dir out
```
EXPECTED:
`test.md` to be written to an `out` subdirectory, not the current directory.
NOTES:
1) This all works as expected if I do
```
touch _quarto.yml
```
to create an empty `_quarto.yml` file.
2) Similarly happens with `--to html` too.
3) `--output-dir` is listed by `quarto render --help`.
ENVIRONMENT:
```
[castedo@quarto-1 1]$ quarto --version
1.1.251
[castedo@quarto-1 1]$ cat /etc/os-release
NAME="Fedora Linux"
VERSION="36 (Container Image)"
ID=fedora
VERSION_ID=36
...
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-29T23:50:23Z",
"creator": "castedo",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2670,
"state": "closed",
"title": "--output-dir option ignored when _quarto.yml file is absent",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2670"
} |
I have 2 students who have installed Quarto and the VSCode extension appropriately but the Render button does nothing, and the keyboard shortcut is not recognized. We can select the drop down menu for rendering different formats, but nothing happens when clicking any of them. It doesn't look "greyed out" either.
The file *will* render if we use the 'quarto preview ".../file.qmd" --to html ' in the terminal.
One user is running Mac OS: Monterey 10.5.1 with Intel i5 processors and are running Python 3.10.7 in VS Code. Not sure what the other student has yet.
Has this come up and been resolved? I can't find anything on this specific issue.
Many thanks! | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-29T21:25:05Z",
"creator": "pcc-git",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3379,
"state": "closed",
"title": "Render Button Inoperable ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3379"
} |
### Bug description
Truly bizzare bug. When you include a mermaid.js diagram on the 1st or second slide of a revealjs presentation it displays fine, but when it's on the 3rd slide or later it requires a refresh to render the diagram.
OS: Mac OS Big Sur 11.6
Rstudio: 2022.07.1 Build 554
This doesn't work properly:
```md
## Slide 1
## Slide 2
## Mermaid slide
This diagram doesn't show up unless you refresh
```{mermaid}
%%| fig-width: 10
flowchart LR
A[Write code] --> B(Source Code)
B --> C{Execute code}
C --> D[Output]
C --> E[Output]
C --> F[Output]
```
```
But this does:
```md
## Slide 1
## Slide 2
## Mermaid slide
This diagram doesn't show up unless you refresh
```{mermaid}
%%| fig-width: 10
flowchart LR
A[Write code] --> B(Source Code)
B --> C{Execute code}
C --> D[Output]
C --> E[Output]
C --> F[Output]
```
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-09-29T16:41:58Z",
"creator": "GShotwell",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2667,
"state": "closed",
"title": "Mermaid diagrams require refresh when they're on the 3rd (!!) slide of a reveal JS presentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2667"
} |
> I want to create custom styles, but it seems the only ones that are available are the Headers.
First, each component in Markdown will be translated in a docx component with a default style apply to them. Best way to see what component (code, list, header, ...) is associated to what style is to add the component in a document, and then compile to docx and look in the resulting document which style is applied. You can use this document as based for tweaking and provide as non default reference doc.
If I understand correctly your use case is also creating new styles from scratch in your template docx document, and then you want to be able to use them (apply them) from your source `.qmd` file.
If that is the case, you can do that for DOCX document using Custom style feature from Pandoc: https://pandoc.org/MANUAL.html#custom-styles. It appears we don't have mention to that in our doc and we should probably add it.
Syntax would be for inline style
````
[Get out]{custom-style="Emphatically"}, he said.
````
and
````markdown
::: {custom-style="Poetry"}
| A Bird came down the Walk---
| He did not know I saw---
:::
````
for paragraph style
You can also reference existing style and not just new one.
Hope it helps
_Originally posted by @cderv in https://github.com/quarto-dev/quarto-cli/discussions/2657#discussioncomment-3763204_
| {
"assignee": null,
"comments": 0,
"created_at": "2022-09-29T14:09:11Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 4502,
"state": "open",
"title": "Document custom styles syntax for using with DOCX template",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4502"
} |
### Bug description
Is it currently possible to get quarto to error on broken links, instead of just warning about them, even if this is opt-in? Having it exit successfully when there are broken cross-links like this makes it harder to include quarto in automated workflows. Especially if multiple people are working on a site, it can mean that these breakages go unnoticed.
Related: https://github.com/r-lib/urlchecker/issues/27
even if it doesn’t error, it would be super useful to print all the broken links at the very end of building a book
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-29T12:30:47Z",
"creator": "allenmanning",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 2665,
"state": "open",
"title": "Quarto should error or warn on broken links",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2665"
} |
### Bug description
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-29T03:12:44Z",
"creator": "zhchenyang",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2663,
"state": "closed",
"title": "Includes not working in asis code chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2663"
} |
### Bug description
On my quarto blog site, on mobile and with very narrow browser windows, there is a lot of space on the right hand side that enables you to “scroll right” to see things off the page. This seems to be needed because I have a few very wide inline `code` words (like `"/Library/Frameworks/R.framework/Versions/Current/Resources/library/cpp11/include"` in the below video)
This actually tends to be very annoying, especially on mobile where it is easy to accidentally swipe right-ish instead of just down. It would be nice if the default was to wrap this instead.
Here is a link to the blog post:
https://blog.davisvaughan.com/posts/2022-03-11-using-vs-code-to-debug-r-packages-with-c-code/
Here is a video of this in action:
https://user-images.githubusercontent.com/19150088/192817190-96ace542-2924-46e4-9dc1-1fc1c2a61a45.mov
---
Garrick suggested I could use this:
```
p code:not(.sourceCode) {
white-space: pre-wrap;
}
```
He showed this image that does suggest that it works
We both think it might be nicer to have this as the default though
---
Quarto v1.2.161 (through qvm)
RStudio 2022.11.0-daily+221 "Elsbeth Geranium" Daily (c11dacb8207aceb03a4e7f11cf0f39360a0733d5, 2022-09-27) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) RStudio/2022.11.0-daily+221 Chrome/102.0.5005.167 Electron/19.0.10 Safari/537.36
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-28T15:16:39Z",
"creator": "DavisVaughan",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2649,
"state": "closed",
"title": "Force wrapping of wide `code` words",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2649"
} |
### Bug description
**Description Issue Render Default R Quarto Document**
Render with yaml extension:
Format: html
Format: pdf
is failing when r code is included
When specifying
Format: docx
it is rendering fine
---
The failed output is shown as:
```
> quarto::quarto_render('T0002.qmd')
Error in rmarkdown:::abs_path(input) :
The file 'T0002.qmd' does not exist.
Calls: .main -> execute -> setwd -> dirname -> <Anonymous>
Execution halted
```
**Code Block:**
````
---
title: "T0002"
format: html
editor: visual
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
## Running Code
When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
```{r}
1 + 1
```
You can add options to executable code like this
```{r}
#| echo: false
2 * 2
```
The `echo: false` option disables the printing of code (only output is displayed).
````
**End**
Rstudio IDE version: RStudio 2022.07.1 Build 554
*** Running on Ubuntu 20.04 and on Windows 10
```
Microsoft Windows [Version 10.0.19042.1706]
(c) Microsoft Corporation. All rights reserved.
C:\Users\bert.Tijhuis>quarto check
[>] Checking Quarto installation......OK
Version: 1.1.163
Path: C:\R\Quarto\bin
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.2
Path: C:/R/Python/Python310/python.exe
Jupyter: 4.10.0
Kernels: python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/R/R-4.2.0
LibPaths:
- C:/R/R-4.2.0/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
C:\Users\bert.Tijhuis>
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 21,
"created_at": "2022-09-28T11:11:53Z",
"creator": "BertTijhuis",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2646,
"state": "closed",
"title": "Render Quarto with HTML or PDF failed in when codechunks with R code are included (Rstudio 2022.07.1 Build 554)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2646"
} |
### Bug description
going to this url:
https://quarto.org/docs/presentations/revealjs/#speaker-notes
produced this output:
<img width="1436" alt="image" src="https://user-images.githubusercontent.com/32404415/192700494-2669c445-a201-42d1-bca0-8dcde277511a.png">
where section header is hidden under navbar
Expected outcome:
section header not hidden under navbar
<img width="1436" alt="image" src="https://user-images.githubusercontent.com/32404415/192700611-500888ca-85d4-4834-b643-3b76365ebe31.png">
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-28T06:06:55Z",
"creator": "miwojc",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2641,
"state": "closed",
"title": "Links to section open with section header hidden below navbar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2641"
} |
### Bug description
I am trying to create a Quarto PowerPoint presentation with a 2-column slide where the columns are not equal width.
I create a source document like below, but the columns are equal width in the rendered PowerPoint document.
The column width settings are respected in `revealjs` and `beamer` format documents.
```
---
title: "Untitled"
format: pptx
editor: visual
---
## Slide title
::: columns
::: {.column width="20%"}
Col 1
x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x
:::
::: {.column width="80%"}
Col 2
x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x x
:::
:::
```
I am using:
Quarto 1.2.160
RStudio 2022.07.2 build 576
Ubuntu 22.04.1
LibreOffice Impress 7.3.6.2 (I don't have PowerPoint on the Ubuntu PC)
PowerPoint 2007 12.0.6776.500 (issue confirmed displaying rendered PowerPoint file on a Windows PC) | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-09-27T23:55:29Z",
"creator": "rgayler",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 2635,
"state": "open",
"title": "can't control column width in 2-column Powerpoint slide",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2635"
} |
### Bug description
See the following document. Removing the centering code or adding a caption leads to the figure's inclusion again.
```md
---
title: "Figure Test"
format: revealjs
---
{fig-align="center"}
```
- OS: Ubuntu 18.04.6 LTS
- RStudio: RStudio 2022.02.1+461 "Prairie Trillium" Release (8aaa5d470dd82d615130dbf663ace5c7992d48e3, 2022-03-17) for Ubuntu Bionic
Mozilla/5.0 (X11; Linux x86_64; rv:104.0) Gecko/20100101 Firefox/104.0
- `quarto::quarto_version()`: `1.2.157`
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-27T16:30:53Z",
"creator": "fkohrt",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2632,
"state": "closed",
"title": "Centered figure without caption not displayed for revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2632"
} |
### Bug description
When I reference a source in Revealjs it appears twice in the end of the presentation. The code looks like:
## Tiden för implementering
::: {#implementering .incremental}
- En ny betygsskala hade nyligen införts.
- Kunskapskrav istället för betygskriterier
- Betygssystemet framstod som icke-kompensatoriskt [@gustafsson2014]
- Proven skulle både stödja lärares betygssättning och bidra till implementering av styrdokumenten.
:::
and the result:
Gustafsson, J.-E., Cliffordsson, C., & Erickson, G. (2014). Likvärdig kunskapsbedömning i och av den svenska skolan – problem och möjligheter (s. 120). SNS - Studieförbundet Näringsliv och Samhälle. https://www.sns.se/aktuellt/likvardig-kunskapsbedomning-i-och-av-den-svenska-skolan-problem-och-mojligheter/
Gustafsson, J.-E., Cliffordsson, C., & Erickson, G. (2014). Likvärdig kunskapsbedömning i och av den svenska skolan – problem och möjligheter (s. 120). SNS - Studieförbundet Näringsliv och Samhälle. https://www.sns.se/aktuellt/likvardig-kunskapsbedomning-i-och-av-den-svenska-skolan-problem-och-mojligheter/
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_6_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
[Presreligion.qmd.zip](https://github.com/quarto-dev/quarto-cli/files/9654984/Presreligion.qmd.zip)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-27T11:32:55Z",
"creator": "frankbach",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2626,
"state": "closed",
"title": "Double references",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2626"
} |
### Discussed in https://github.com/quarto-dev/quarto-web/discussions/414
<div type='discussions-op-text'>
<sup>Originally posted by **e-alizadeh** September 26, 2022</sup>
I want to remove the BibTeX citation section at the end of my post, but want to keep the attribution piece as shown in the screenshot.
Currently, I'm using the `citation: true` in the `_metadata.yml` file. If I set it to `false`, both the BibTeX citation and the attribution box will disappear.
Thanks in advance
</div> | {
"assignee": null,
"comments": 0,
"created_at": "2022-09-27T11:08:11Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 2625,
"state": "closed",
"title": "Allow user to specify whether to show bibtex, html, or both citation formats in HTML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2625"
} |
### Bug description
I was trying to publish a document contained in a subfolder to Quarto Pub, e.g.
```
quarto publish quarto-pub folder/test.qmd
```
The structure is:
```
.
└── folder
└── test.qmd
```
And the content of `folder/test.qmd` is not important, e.g.
```
---
engine: jupyter
---
## Test
This is a simple test file.
```
But this didn't work, because after entering the account and document name, I got this error:
```
ERROR: NotFound: No such file or directory (os error 2), stat 'folder/folder/test_files/libs'
```
FWIW, this was a document rendered with the `jupyter` engine (but I get the same error with `knitr`), and I was running Quarto 1.1.251 on macOS.
Also, `quarto preview folder/test.qmd` is working, and publishing from within the `folder` also works.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-09-27T08:12:16Z",
"creator": "cbrnr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2623,
"state": "closed",
"title": "quarto publish in subfolder fails",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2623"
} |
### Bug description
Hi,
I have a quarto presentation with `Altair` plot and `OJS`.
For some reason, the Altair plots do not consistently show up on chromium-based browsers (I tested Microsoft Edge and Google Chrome). Weirdly, on Firefox, it works fine.
If I keep refreshing a bunch of times, eventually it works
I published the slides [here](https://lourenzutti.quarto.pub/altair--ojs----error/#/slide-with-altair-plot)
Here's the code for
````md
---
title: "Altair + OJS -- Error"
format: revealjs
---
```{python}
import pandas as pd
import altair as alt
from vega_datasets import data
```
## Slide with altair plot
```{python}
cars = data.cars()
alt.Chart(cars)\
.mark_point()\
.encode(
x = 'Horsepower:Q',
y = 'Miles_per_Gallon:Q')
```
## OJS
```{ojs}
data = [{'x': 1, 'y': 1}, {'x': 2, 'y': 2}];
Plot.plot({
marks: [
Plot.dot(data, {x: "x", y: "y"})
]});
```
````
OS: Windows 11 (21H2)
Editor: RStudio (2022.07.1+554) and vscode -- I tried both
Quarto: 1.2.157
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-09-27T05:15:53Z",
"creator": "Lourenzutti",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "v1.4",
"number": 2621,
"state": "open",
"title": "Altair plots disappearing with OJS cells on Chromium-based Browser",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2621"
} |
### Bug description
If the first paragraph of a page contains formatting (bold for example) the listing layout breaks. I tried with a page (among a number of other pages without formatting) that contains some bold first paragraph like so:
```md
---
title: "Test1"
---
**Lorem ipsum dolor sit amet, consectetur adipiscing elit. Proin maximus turpis id neque pharetra, ut vehicula augue sagittis. Duis pellentesque dolor vel diam imperdiet lacinia.**
Nulla facilisi. Morbi placerat faucibus mauris a luctus. Donec pellentesque mauris auctor tortor laoreet maximus. Maecenas ac risus in turpis suscipit euismod. Cras id congue nibh. Donec efficitur risus nec velit convallis consectetur. Morbi tincidunt non urna non ornare.
```
In a grid listing the cards are stuck in two columns. In a blog style the "columns" break.
I am using Quarto 1.2.157 on Mac OS 12.6.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-09-27T04:42:32Z",
"creator": "Nenuial",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2620,
"state": "closed",
"title": "Formatting breaks listing layout",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2620"
} |
### Bug description
Unicode can be displayed in the body, but not in the title and headings
```
---
title: 青黑體
format: pdf
mainfont: "Noto Sans CJK JP"
---
## 青黑體簡體中文,ヒラギノ
青黑體簡體中文,ヒラギノ角
```
os version
```
NAME="Ubuntu"
VERSION="20.04.4 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.4 LTS"
```
quarto version
```
quarto check
[✓] Checking Quarto installation......OK
Version: 1.1.251
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....OK
Version: 3.8.13 (Conda)
Path: /home/xx/anaconda3/bin/python
Jupyter: 4.10.0
Kernels: python2, ir, python3
[✓] Checking Jupyter engine render....OK
[✓] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.16
[✓] Checking Knitr engine render......OK
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-09-27T02:23:06Z",
"creator": "zhchenyang",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2619,
"state": "closed",
"title": "Unicode cannot be displayed in headings and title",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2619"
} |
### Bug description
I have a slide where I show two steps with a pause between the two. If I add a footnote in the second step, it is displayed from the beginning whereas it should appear only in the second step.
Example:
```rmd
---
format: revealjs
---
First step.
. . .
Second step^[This footnote shouldn't appear in the first step.]
```
---
RStudio 2022.07.1+554 "Spotted Wakerobin"
quarto v. 1.2.157
Windows 10 x64 (build 19044)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-26T17:39:38Z",
"creator": "etiennebacher",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "Future",
"number": 2616,
"state": "open",
"title": "revealjs: footnotes always appear despite pauses",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2616"
} |
This page is currently an orphaned page: https://quarto.org/docs/output-formats/html-themes-more.html - it has no left-sidebar.
The link to this page can be seen at: https://quarto.org/docs/output-formats/html-themes.html#:~:text=For%20more%20information%20about%20available%20Sass%20variables%2C%20see
May need to be added at: https://github.com/quarto-dev/quarto-web/blob/main/_quarto.yml#L142-L149 ?
| {
"assignee": null,
"comments": 1,
"created_at": "2022-09-26T17:00:36Z",
"creator": "jthomasmock",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4503,
"state": "closed",
"title": "\"HTML themes more\" article not linked to sidebar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4503"
} |
### Bug description
Working with an **.ipynb** file in **VSCode**. Quarto **0.9.462**. Windows 11.
To reproduce, use the Python package `statsmodels` to generate a summary of an OLS model. That is,
```python
import pandas as pd
import statsmodels.formula.api as smf
df = pd.read_csv("Carseats.csv") # The one included in ISLR
mod1 = smf.ols(formula='Sales ~ Price + Urban + US', data=df)
res1 = mod1.fit()
res1.summary()
```
Then you get 2 tables
Now render PDF with Quarto
You only get one table.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-09-26T16:57:47Z",
"creator": "JER-ry",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2615,
"state": "closed",
"title": "My code generated two tables, but Quarto only handled one",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2615"
} |
### System details
RStudio Edition: Desktop
RStudio Version : 2022.07.1 Build 554
OS Version : MacOS 12.6
R Version : 4.2.1
### Steps to reproduce the problem
1. Create a new Quarto Presentation
2. Set the output to revealjs, and `df-print` to `paged`
3. Add a slide with an r chunk calling a data frame
5. Render the presentation
Minimal example:
````
---
title: "Untitled"
format:
revealjs:
df-print: paged
editor: visual
---
## Cars Data
```{r}
cars
```
````
### Describe the problem in detail
The page scroller is not visible in presentation format. I can only see the first 8 rows and the rest gets cut off. When I change the format to HTML it appears to be working fine.
### Describe the behavior you expected
I expect the font to be rescaled for this `df_print: paged` option so to that the entire table (10 rows + scrolling bar) are visible.
- [ ] I have read the guide for [submitting good bug reports](https://github.com/rstudio/rstudio/wiki/Writing-Good-Bug-Reports).
- [x ] I have installed the latest version of RStudio, and confirmed that the issue still persists.
- [ ] If I am reporting an RStudio crash, I have included a [diagnostics report](https://support.rstudio.com/hc/en-us/articles/200321257-Running-a-Diagnostics-Report).
- [ x] I have done my best to include a minimal, self-contained set of instructions for consistently reproducing the issue.
| {
"assignee": null,
"comments": 0,
"created_at": "2022-09-26T13:41:08Z",
"creator": "vrbiki",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3380,
"state": "closed",
"title": "Data frame paged print out too large in revealjs format",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3380"
} |
### Bug description
Mermaid diagrams in reveal JS clip the diagram image after the second slide.
For example, consider the following file (named slides.qmd):
````
---
title: "mermaid crash"
format:
revealjs
---
# git graph 1
```{mermaid}
gitGraph
commit id: "Alpha"
```
# git graph 2
```{mermaid}
gitGraph
commit id: "Alpha"
```
# git graph 3
```{mermaid}
gitGraph
commit id: "Alpha"
```
````
Creates the expected output for git graph 1 and 2, which look like this:
But slide 3 looks like this (as do any subsequent slides with mermaid content):
I am using the latest nightly build (1.2.157) on Ubuntu 20.04. I am just using quarto from the command line to generate the html (no R studio).
I get the same problem when viewer rendered html with Chrome or Firefox. Also, it is not unique to gitGraph, any mermaid content gets distorted and clipped. Interestingly, sometime while in preview mode the problem rights itself after making a change to any of the slides (but not always).
Thanks!
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 11,
"created_at": "2022-09-26T02:29:48Z",
"creator": "d-chambers",
"is_pull_request": false,
"labels": [
"bug",
"mermaid"
],
"locked": false,
"milestone": "v1.2",
"number": 2607,
"state": "closed",
"title": "Mermaid diagrams in reveal JS don't render after 2nd slide",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2607"
} |
### Bug description
Since I installed the Quarto preview version 1.2.154, the descriptions in grid listings seem to be far too long. I tried using `max-description-length` to shorten them, but to no effect. It seems to take the entire first paragraph of the page.
I'm using Quarto 1.2.154 on MacOS 12.6 using 2022.07.1 Build 554.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-09-25T15:36:57Z",
"creator": "Nenuial",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2604,
"state": "closed",
"title": "Grid listing description length is too long",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2604"
} |
### Bug description
````md
---
title: "Quarto Latex Issue Docx"
format: docx
---
$$
\text{Level 1: } Y_{ij} = \beta_j +\epsilon_{ij} \\
\text{Level 2: } \beta_j = \gamma + \delta_j \\
\text{Reduced Form: } Y_{ij} = \gamma + \delta_j + \epsilon_{ij}
$$
```{r}
sessionInfo()
```
````
This is my `sessionInfo()`
```{r}
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8
[4] LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flextable_0.7.3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 digest_0.6.29 R6_2.5.1 evaluate_0.16 zip_2.2.0
[6] rlang_1.0.4 gdtools_0.2.4 cli_3.3.0 uuid_1.1-0 data.table_1.14.2
[11] rstudioapi_0.14 xml2_1.3.3 rmarkdown_2.16 tools_4.2.1 officer_0.4.3
[16] yaml_2.3.5 xfun_0.32 fastmap_1.1.0 compiler_4.2.1 systemfonts_1.0.4
[21] base64enc_0.1-3 htmltools_0.5.3 knitr_1.40
```
The docx outputs this: `$$ \text{Level 1: } Y_{ij} = \beta_j +\epsilon_{ij} \\ \text{Level 2: } \beta_j = \gamma + \delta_j \\ \text{Reduced Form: } Y_{ij} = \gamma + \delta_j + \epsilon_{ij} $$`
instead of latex-rendered math
RStudio: `"Spotted Wakerobin" Release (7872775e, 2022-07-22) for Ubuntu Jammy`
May be related [to this bug](https://github.com/quarto-dev/quarto-cli/issues/2601)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-09-25T13:39:38Z",
"creator": "emstruong",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": null,
"number": 2602,
"state": "closed",
"title": "DOCX not rendering Latex",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2602"
} |
### Bug description
````md
---
title: "Quarto Latex Issue PDF"
format: pdf
---
$$
\text{Level 1: } Y_{ij} = \beta_j +\epsilon_{ij} \\
\text{Level 2: } \beta_j = \gamma + \delta_j \\
\text{Reduced Form: } Y_{ij} = \gamma + \delta_j + \epsilon_{ij}
$$
```{r}
sessionInfo()
```
````
This is my `sessionInfo()`
```{r}
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C LC_TIME=en_CA.UTF-8
[4] LC_COLLATE=en_CA.UTF-8 LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flextable_0.7.3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 digest_0.6.29 R6_2.5.1 evaluate_0.16 zip_2.2.0
[6] rlang_1.0.4 gdtools_0.2.4 cli_3.3.0 uuid_1.1-0 data.table_1.14.2
[11] rstudioapi_0.14 xml2_1.3.3 rmarkdown_2.16 tools_4.2.1 officer_0.4.3
[16] yaml_2.3.5 xfun_0.32 fastmap_1.1.0 compiler_4.2.1 systemfonts_1.0.4
[21] base64enc_0.1-3 htmltools_0.5.3 knitr_1.40
```
The pdf outputs into a single line: Level 1:𝑌𝑖𝑗= 𝛽𝑗+ 𝜖𝑖𝑗Level 2:𝛽𝑗= 𝛾 + 𝛿𝑗Reduced Form:𝑌𝑖𝑗= 𝛾 + 𝛿𝑗+ 𝜖𝑖𝑗
When it seems like it should be broken up
RStudio: `"Spotted Wakerobin" Release (7872775e, 2022-07-22) for Ubuntu Jammy`
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-09-25T13:37:09Z",
"creator": "emstruong",
"is_pull_request": false,
"labels": [
"bug",
"upstream",
"third-party"
],
"locked": false,
"milestone": "Future",
"number": 2601,
"state": "open",
"title": "PDF output does not respect Latex Line Breaks in Math",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2601"
} |
### Bug description
Hello,
After the 1.2.145 update, I cannot render python. Even if environment variables was set, it gives error "unable to locate python". I tried to update to latest prerelease but problem still continue.
`python` command is available from same terminal.
Quarto version: 1.2.145 - 1.2.154
RStudio version: 2022.07.1 Build 554
OS: Win 10 Pro Version 10.0.19044 Build 19044
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-25T12:07:47Z",
"creator": "mrtkp9993",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2599,
"state": "closed",
"title": "Python rendering not working after update",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2599"
} |
### Bug description
Quotation (">") does not work when using pdf-output, Ther is no grey line and grey textcolor .
> Test
### System
I am using Windows and VS Code
| {
"assignee": null,
"comments": 1,
"created_at": "2022-09-25T09:37:39Z",
"creator": "benjaminmoritz",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2598,
"state": "closed",
"title": "Quotation (\">\") does not work when using pdf-output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2598"
} |
## Premise
Hi everyone! I would like to thank the **RStudio** and the **QUARTO** _community_ for being here and for all the amazing tools and support provided.
I am currently trying to write my _Master's degree thesis_ in **QUARTO**. I am absolutely excited about this great piece of software. Nevertheless, there are problems that puzzle me, at least.
<span style="color: red;">**WARNING**</span> : **_this is going to be a long one_**, but indeed I hope that if solutions are provided to the following doubts and questions it may be of great aid for that part of community interested in the **PDF format** output.
Just so you know: there is no title-author-date info in the **quarto.YML** header I provide here because I am adding it afterwards with a custom titlepage I wrote in `LaTex`.
### Operating System
Windows 11 Pro (x64) Build 22000
### IDE
**RStudio** 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for Windows
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.8 Chrome/69.0.3497.128 Safari/537.36
### QUARTO version
(It is the one that comes with RStudio):
```r
quarto_version()
[1] ‘1.1.189’
```
### My `quarto check` output:
```
[>] Checking Quarto installation......OK
Version: 1.1.189
Path: C:\Program Files\RStudio\bin\quarto\bin
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.6
Path: C:/Python/Python310/python.exe
Jupyter: 4.11.1
Kernels: python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.2.1
Path: C:/R/R-4.2.1
LibPaths:
- C:/R/R-4.2.1/library
rmarkdown: 2.16
[>] Checking Knitr engine render......OK
```
## Bugs and questions list
### 1
Specifying the `output-dir:` behaves weirdly. What's odd about it is that in case I changed my mind and wanted back the compiled project .pdf file in the root directory and thence comment or delete this entry out of the **YML** header... it just ignores it and still renders the book to the previously specified output (a subfolder I named **_book**). While formatting the appearence of this document I noticed that sometimes it helped to close and reopen the project to make **YML** options work. Yet unfortunately, this is not the case with regard to the problems I list here. By the way, is there perhaps some such thing as a "_QUARTO-project related cache_" that can be cleared out?
### 2
Even though I entered a `latex-output-dir:` option, specifying a subdirectory i created (**_tex-docs**), only **index.qmd** related files (such as **index.tex**, **index.log**, **index.lof**, etc.) are moved in there after compilation, while having the .tex file of the entire document in the root directory of the project (the main folder).
### 3
Not having set a title in the YML the outpout obtained is a PDF file named after the name of the project's folder itself. One may try to change this behaviour with: `output-file: "a-name"` and `output-ext: pdf`. In my experience they always get ignored.
### 4
Doubt about the ` fig-pos ` option. Instead of the `:` colon, should one use the `=` equal sign as per the example [here in the docs](https://quarto.org/docs/reference/formats/pdf.html#figures)?
### 5
I am letting a ` LaTex ` preamble do geometry and font related jobs, except for the font name itself which I had troubles with setting it via a ` \fontspec{Arial} ` command. Is it better to rely on the corresponding YML options for geometry and font customization, or is it something acceptably interchangeable?
### 6
I happen to have a doubt about the `linkcolor:` option. #Documentation states that _**[any x11 color](https://quarto.org/docs/reference/formats/pdf.html#colors)** should be available_. Nevertheless, **none of the x11 color names I tried worked**, resulting in a rendering error. Is it my fault? Am I typing them wrong? Is there an officail list for all the x11 colors?
### 7
If, for instance, I'd like to add everything i have in my **.bib** with an explicit nocite: | @* statement in the **YML** this command adds up entries to the existing ones printed by in-text **references** (quotations to elements of the provided bibliography **.bib** file called by the `@` operator inside main text or in footnotes). The result is that if I **already cited** an author inside the body of my document, passing a `nocite: @*` command in the **YML** _makes the bibliographic reference to the **same author appear two times**_, also weirdly removing the author's name in the repeated entry with a set of dashes, as may hopefully observe looking at the following snip.
### 8
Sometimes the suggestions for **autocompletion** of **YML** metadata entries **do not pop up**, even after closing and reopening the project several times. The only fix happened to be a machine reboot.
### 9
In different occasions (in my real quarto project which has more content) I managed to change the pagestyle by, for instance, adding a ` \pagestyle{empty} ` or ` \thispagestyle{empty} ` at the beginning of the **.qmd** file containing the section I would have liked to be rendered without headers nor footers nor page numbers. Nonetheless I tried to do this in my **references.qmd** file **but header and footer are still rendered for that section**. I know I added a command in the **preamble.tex** to make headers and footers to be printed on the heading page (as opposite to the default `LaTeX` behaviour), however this woulkd be of no concern at all at the moment I command the page-style to be empty at the beggining of the section (just before the heading entry).
### 10
**QUARTO** "_**Renders on save**_" everytime I save (of course...) even though I toggle off the option ticking out the little box that's on the toolbar of the **Rstudio IDE** file reader for **.qmd** files. That's annoying, and it just happened after I tried reinstalling RStudio to check if this would have fixed the issues I am currently facing... eventually adding another one to the list. _Moreover, I noticed the automatic render on save behaviour when modifying and saving the_ **YML** _header file itself or_ **.tex** _files related to the_ **YML** metadata opened as tab inside the **RStudio IDE**, such as preamble.tex, which by the way do not have that tick box to toggle on or off on their toolbar pane.
### 11
How can one **center a piece of text** for the **.pdf** format? Doing the following still **doesn't** produce a centered output in the pdf. And... yes, I've tried to write this in `CSS` syntax, with absolutely no success at all.
````md
::: {align="center"}
# Introduzione {.unnumbered}
:::
````
### 13
If I'd like to change the way how `number-sections` works, for instance, using roman numerals or restarting the sections' count for a part of my document is it possible to use `tex` code to this right inside (at the beginning of) the corresponding **.qmd** files? Or am I required to make use of **partials** for things like these?
## Files list
Here are a **_quarto.YML** file and a **preamble.tex** right below. I tried to strip down these two files to the best of my ability (Removed unnecessary entries that would not affect the software's behaviuor, still causing the bugs I discussed above), thence something may semantically make no sense (as language, casue for the italian localization I use a self-made language.yml file which is omitted here). Down below I've written the content of the other relevant files too.
### MY MWE "_quarto.YML"
```YML
project:
type: book
#output-dir: _book
book:
chapters:
- index.qmd
- 6_risorse.qmd
bibliography: |
- bibiliografia_lm56.bib
csl: quad_mat_edit.csl
notes-after-punctuation: true
links-as-notes: true
link-citations: true
callout-appearance: default
nocite: |
@*
format:
pdf:
pdf-engine: xelatex
documentclass: scrbook
classoption: [12pt,headsepline,footsepline,oneside,headings=small]
mainfont: ArialMT
fontsize: 12pt
monofont: ArialMT
toc-title: Indice dei contenuti
toc: true
number-sections: false
number-depth: 5
df-print: kable
code-line-numbers: true
fig-align: center
fig-pos: "H"
highlight-style: pygments
output-file: "tesi-lm56" #This just gets ignored
output-ext: "pdf" #This too
template-partials:
- toc.tex
- after-body.tex
include-in-header: my_YML_LaTeX_preamble.tex
include-after-body:
text: |
\printindex
colorlinks: true
linkcolor: RoyalBlue4 #Am I typing x11 colors in wrong way? Is there an official list?
filecolor: RoyalBlue4
citecolor: RoyalBlue4
urlcolor: RoyalBlue4
toccolor: black
standalone: true
keep-tex: true
keep-ipynb: true
latex-auto-mk: true
latex-auto-install: true
latex-clean: false
latex-output-dir: _tex-docs
editor: visual
```
### MY MWE "preamble.tex"
```tex
\usepackage[english,main=italian]{babel}
\usepackage[a4paper, twoside, inner=4.5cm, outer=3cm, top=3.5cm, bottom=3.5cm]{geometry}
\usepackage{setspace}
\setstretch{1.5}
\setparsizes{1cm}{1cm}{1cm plus 1fil}
\usepackage[hang]{footmisc}
\renewcommand{\footnotelayout}{\setstretch{1.1}}
\addtolength{\skip\footins}{2pt}
\setlength{\footnotesep}{12pt}
\usepackage{xpatch}
\makeatletter
\xpatchcmd{\deffootnote}{\hbox to \z@}{\hbox}{}{\undefined}
\makeatother
\deffootnote[0.6cm]{0em}{1em}{\thefootnotemark.\ }
\RedeclareSectionCommand[tocbeforeskip=2ex plus 2pt minus 1pt]{chapter}
\makeatletter
\renewcommand*{\@pnumwidth}{1em}
\makeatother
\usepackage{indentfirst}
\usepackage{amsmath}
\usepackage{makeidx}
\makeindex
\addtocontents{toc}{\protect\thispagestyle{empty}}
\addtocontents{lof}{\protect\thispagestyle{empty}}
\addtocontents{lot}{\protect\thispagestyle{empty}}
\usepackage{afterpage}
\usepackage{scrlayer}
\usepackage{tocloft}
\setlength{\cftchapindent}{-20pt}
\usepackage{scrlayer-scrpage}
\pagestyle{scrheadings}
\usepackage{kantlipsum}
\renewcommand*{\chapterpagestyle}{headings}
```
### My toc.tex
```tex
$if(toc)$
$if(toc-title)$
\renewcommand*\contentsname{$toc-title$}
$endif$
$if(beamer)$
\begin{frame}[allowframebreaks]
$if(toc-title)$
\frametitle{$toc-title$}
$endif$
\tableofcontents[hideallsubsections]
\end{frame}
$else$
{
$if(colorlinks)$
\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
$endif$
\setcounter{tocdepth}{$toc-depth$}
\tableofcontents
}
$endif$
$endif$
\newpage
```
### My _index.qmd
````md
```{=tex}
\pagestyle{scrheadings}
\pagenumbering{Roman}
```
::: {align="center"}
# Introduzione {.unnumbered}
:::
\kant[1-2].[^1_capitolo-1]
[^1_capitolo-1]: This is an example footnote reference to [@khuri2003] pp. xx
````
**My references.qmd**
````md
\pagenumbering{gobble} #This should remove the `scrheadings`, yet it does not
\pagestyle{empty}
# Risorse {.unnumbered}
::: {#refs}
:::
````
### My "dummy" references .bib file content for this MWE to run
```
@book{khuri_advanced_2003,
address = {Hoboken, N.J},
edition = {2nd ed., rev. and expanded},
series = {Wiley series in probability and statistics},
title = {Advanced calculus with applications in statistics},
isbn = {978-0-471-39104-3},
publisher = {Wiley-Interscience},
author = {Khuri, André I.},
year = {2003},
keywords = {Calculus, Mathematical statistics},
}
@book{ochsner_advanced_2021,
address = {Cham, Switzerland},
title = {Advanced {LaTeX} in academia: applications in research and education},
isbn = {978-3-030-88956-2},
shorttitle = {Advanced {LaTeX} in academia},
abstract = {This book contains a comprehensive treatment of advanced LaTeX features. The focus is on the development of high quality documents and presentations, by revealing powerful insights into the LaTeX language. The well-established advantages of the typesetting system LaTeX are the preparation and publication of platform-independent high-quality documents and automatic numbering and cross-referencing of illustrations or references. These can be extended beyond the typical applications, by creating highly dynamic electronic documents. This is commonly performed in connection with the portable document format (PDF), as well as other programming tools which allow the development of extremely flexible electronic documents},
language = {eng},
publisher = {Springer},
author = {Öchsner, Marco and Öchsner, Andreas},
year = {2021},
note = {OCLC: 9408012663},
}
@book{lantz_machine_2019,
address = {Birmingham Mumbai},
edition = {Third edition},
title = {Machine learning with {R}: expert techniques for predictive modeling},
isbn = {978-1-78829-586-4},
shorttitle = {Machine learning with {R}},
language = {eng},
publisher = {Packt Publishing},
author = {Lantz, Brett},
year = {2019},
}
@book{khuri2003,
title = {Advanced calculus with applications in statistics},
author = {Khuri, {André I.}},
year = {2003},
date = {2003},
publisher = {Wiley-Interscience},
series = {Wiley series in probability and statistics},
edition = {2nd ed., rev. and expanded},
address = {Hoboken, N.J}
}
```
## MANY THANKS YOU TO YOU ALL!
If there is something here that is supposed to work as I am currently experiencing and have showcased in here, please let me know: I'm really not here to assume that something is a bug when infact it is a feature, I just want to understand.
### Checklist
- [x] Include the terminal output of `quarto check`
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-09-24T20:53:40Z",
"creator": "Nicholas-R-Sheriff",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 2596,
"state": "open",
"title": "Several Bugs Report for the .pdf format output + doubts",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2596"
} |
### Bug description
It seems like macros in hidden divs still get expanded by pandoc. This is problematic as I have defined some macros that only work with mathjax not latex (and vis versa) (for example the mathjax mathtip macro)
```quarto
::: {.content-visible unless-format="pdf"}
\newcommand{\test}{one}
:::
::: {.content-visible unless-format="html"}
\newcommand{\test}{two}
:::
$\test$
```
Quarto will complain that the second macro has already been defined irrespective of output. Ideally for macros one should be able to have a sort of preamble for html that gets parsed by pandoc (not just passed through like include-before-body does), thus one could specify which to include in yaml dependent on output wanted
| {
"assignee": null,
"comments": 1,
"created_at": "2022-09-23T15:35:26Z",
"creator": "lcnbr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2580,
"state": "open",
"title": "Conditional content does not work with latex macros",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2580"
} |
I'd like to use Listings to present specific content on a page based on either category or tag (I'll use which ever is easier to implement).
I can almost get there today -- with `categories: true` as a site visitor I can click on a category and see my filtered list of content, however, I don't want this to be a site visitor action, as the site author I want to only show certain content based on tag.
Ultimately I want to have a page with multiple listings, each listing defined by category. | {
"assignee": "dragonstyle",
"comments": 2,
"created_at": "2022-09-23T14:11:20Z",
"creator": "kmasiello",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 2577,
"state": "closed",
"title": "Website listings - filter by category",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2577"
} |
### Bug description
When I add the lines
```{python}
#| label: fig-density
#| fig-cap: "Plots of the probability density function for $\mu$ = 10"
```
in a `{python}` block, then render my project with VSCode (`❯ quarto preview /path/to/project --render all --no-browser --no-watch-inputs`), I get the error
```
Rendering:
ERROR: YAMLException: unknown escape sequence (undefined, 3:59)
3: fig-cap: "Plots of the probability density function for $\mu$ = 10"
```
which is somehow caused by having the math environment in the caption. Is there a simple way around this? I couldn't find anything in the docs.
Quarto 1.0.38, MacOS Monterey 12.5.1, M1 MacBook Air
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-23T13:19:47Z",
"creator": "phinate",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2576,
"state": "closed",
"title": "\"Unknown escape sequence\" error when rendering dollar sign math syntax in figure caption",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2576"
} |
@cderv It does seem like we should consider doing this when rsvg-convert is available on the path. We'd just need a Lua filter for this that targets PDF/LaTeX/Beamer. I'd think we'd want to do it automatically (as the other alternative is an error message from LaTeX). Could you take a shot at a PR for this? (note that the node module requires native code so not something we can easily port to deno).
cc @cscheid
_Originally posted by @jjallaire in https://github.com/quarto-dev/quarto-cli/issues/997#issuecomment-1140310275_
## Context
This is what Pandoc is [doing in its PDF writer](https://github.com/jgm/pandoc/blob/b263f383040618ff991912512ccd396b83d43da5/src/Text/Pandoc/PDF.hs#L194-L205), and we should probably bring this feature back for our `quarto render --to pdf` format, as this is a difference from `pandoc --to pdf` behavior. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-23T11:54:56Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"pandoc-lua"
],
"locked": false,
"milestone": "v1.3",
"number": 2575,
"state": "closed",
"title": "Use rsvg-convert when available on the path to convert SVG to PDF like Pandoc",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2575"
} |
### Bug description
Quarto does not seem to allow any styling of the text in table captions like _italics_ etc.
This problem does not occur with figure captions.
### Screenshot
### .qmd file (can't attach):
````
---
title: "No markdown styling in table caption"
format:
html:
theme: default
keep-md: true
---
```{r}
# captions for figure and table with md styling
caption_table <- "Can't use ^superscript^ or _italics_ in table caption"
caption_figure <- "Can use ^superscript^ or _italics_ in figure caption"
```
```{r}
#| tbl-cap: !expr caption_table
# caption is set in qmd with: #| tbl-cap: !expr caption_table
library(kableExtra)
column_spec(kable(head(cars)),column = 1:2, width = "15em")
```
```{r}
#| fig-cap: !expr caption_figure
# caption is set in qmd with: #| tbl-cap: !expr caption_figure
plot(cars)
```
```{r}
sessionInfo()
```
````
Table captions are put inside some sort of div, which ignores markdown synthax (or latex syntax when rendering to pdf), for this reason I included the intermediate .md file.
### .md file excerpt (also see attachment):
````
::: {.cell tbl-cap='Can\'t use ^superscript^ or _italics_ in table caption'}
```{.r .cell-code}
# caption is set in qmd with: #| tbl-cap: !expr caption_table
library(kableExtra)
column_spec(kable(cars),column = 1:2, width = "15em")
```
::: {.cell-output-display}
....
````
[reprex_table_formatting.md](https://github.com/quarto-dev/quarto-cli/files/9632422/reprex_table_formatting.md)
### Info
Rstudio IDE: 2021.09.0 Build 351
Session info:
```
R version 4.1.3 (2022-03-10)
Platform: x86_64-re
dhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.5 (Ootpa)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.15.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] kableExtra_1.3.4
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 knitr_1.39 xml2_1.3.3 magrittr_2.0.3
[5] rvest_1.0.2 munsell_0.5.0 viridisLite_0.4.0 colorspace_2.0-3
[9] R6_2.5.1 rlang_1.0.5 fastmap_1.1.0 highr_0.9
[13] stringr_1.4.0 httr_1.4.3 tools_4.1.3 webshot_0.5.3
[17] xfun_0.31 cli_3.3.0 systemfonts_1.0.4 htmltools_0.5.2
[21] yaml_2.3.5 digest_0.6.29 lifecycle_1.0.1 htmlwidgets_1.5.4
[25] glue_1.6.2 evaluate_0.15 rmarkdown_2.14 stringi_1.7.6
[29] compiler_4.1.3 scales_1.2.0 jsonlite_1.8.0 svglite_2.1.0 ****
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 6,
"created_at": "2022-09-23T09:27:17Z",
"creator": "patrickvdb",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": "v1.3",
"number": 2573,
"state": "closed",
"title": "Markdown styling in table captions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2573"
} |
### Bug description
I see some unexpected behavior when it comes to cross-referencing and linking to chapters and sections in book parts.
- When I have a cross-reference to a chapter / level 1 header in a book part, it does not work for html or pdf.
- When I have a level 2 header in a book part, it does not appear to work at all for pdf output, but a cross-reference to a level 2 header works for html output.
- When I have a hyperlink to a chapter / level 1 header in a book part, the link appears in the pdf output but it does not link anywhere. In html it works fine.
- When I have a hyperlink to a level 2 header in a book part, it works in html and pdf.
part_x.qmd:
````
# Part X {#sec-part-x}
## section x.1 {#sec-part-x-section-1}
````
chapter_y.qmd:
````
# Chapter y
Cross-ref to a level 1 header in a part: @sec-part-x
Cross-ref to a level 2 header in a part: @sec-part-x-section-1
Hyperlink to a level 1 header in a part: [part x](part_x.qmd) (The link appears in pdf, but does not work. in html it works)
Hyperlink to a level 2 header in a part: [part x section x.1](part_x.qmd#sec-part-x-section-1)
````
html output for chapter y:
pdf output for chapter y:
quarto_1.2
Rstudio daily: 2022.11.0 Build 202 (also used build 83)
R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 9,
"created_at": "2022-09-23T08:20:56Z",
"creator": "VMTdeJong",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2571,
"state": "open",
"title": "Cross-reference and link to book parts",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2571"
} |
### Bug description
👋 thanks again for quarto. the more i use it, the more i am appreciating it.
I am reporting this here with quarto rather than knitr because it changes for me from `1.1.251` -> `1.2.148`.
I also tested on the dev version with this HEAD (https://github.com/quarto-dev/quarto-cli/commit/5da03618fedf82742fac3635364a8074f11d3d3e) and the issue was this present. As of `1.2.148` I can't knit child qmds that are in a separate folder. I can reproduce with these two files:
````md
---
title: "Untitled"
execute:
eval: true
echo: false
warning: false
format: html
---
```{r r-pkgs}
library(dplyr)
library(gt)
library(purrr)
```
# Tables
::: {.panel-tabset}
```{r}
#| output: asis
res <- purrr::map_chr(unique(starwars$homeworld), \(hw) {
knitr::knit_child(
input = "child-dir/_child.qmd",
envir = environment(),
quiet = TRUE
)
})
cat(res, sep = '\n')
```
:::
````
### child-dir/_child.qmd
````md
## `r hw`
```{r}
#| echo: false
starwars %>%
filter(homeworld == hw) %>%
count(sex) %>%
head() %>%
gt()
```
````
Here is the error I am getting:
> Error in readLines(con, warn = FALSE) : cannot open the connection
Calls: .main ... <Anonymous> -> enumerate_output_formats -> read_utf8 -> readLines
In addition: Warning message:
In readLines(con, warn = FALSE) :
cannot open file '_child.qmd': No such file or directory
>
> Execution halted
This works if the child qmds are in the same directory as the main qmd.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 12,
"created_at": "2022-09-22T21:17:14Z",
"creator": "boshek",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 2566,
"state": "closed",
"title": "Can't knit child qmds in a sub-directory",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2566"
} |
The sidebar nav `content: auto` functionality does not list index.(q/r)md files as pages in the navigation menu. For sites that are organized with content pages within individual folders, each with an index file inside, the sidebar navigation will be blank when using any of the auto generation options.
| {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-09-22T21:00:39Z",
"creator": "kmasiello",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2565,
"state": "closed",
"title": "Sidebar nav `auto` population does not pull in index files",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2565"
} |
### Bug description
Dear support team,
I have come across a wired behavior of Quarto Book (in Rstudio) when using `bash` chunks. I initiate quarto book project from Rstudio and if I include `bash` chunks in the qmd files which are initiated with the project (index.qmd, intro.qmd etc) it works fine. However, if I create new .qmd file (File > New File > Quarto Document) and include the same `bash` chunk, it throws the following error:
```
[4/5] test1.qmd
Starting python3 kernel...Traceback (most recent call last):
File "/Applications/quarto/share/jupyter/jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "/Applications/quarto/share/jupyter/notebook.py", line 16, in <module>
import nbformat
ModuleNotFoundError: No module named 'nbformat'
Python 3 installation:
Version: 3.8.9
Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
```
R studio: 2022.07.1 Build 554
Operating system: macOS Big Sur; version 11.6.6
What could be the problem?
Kind regards,
Amel
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-09-22T15:24:32Z",
"creator": "AmelZulji",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2557,
"state": "closed",
"title": "bash code chunks error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2557"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2512
<div type='discussions-op-text'>
<sup>Originally posted by **iusgit** September 20, 2022</sup>
Hi,
first thanks for this wonderful tool!
I created a book project and one output format is a docx (unfortunately... I'm not a friend of this, but the project commands it).
My book looks like this:
```
book:
chapters:
- index.qmd
- content/Chapter_01.qmd
- content/Chapter_02.qmd
```
File `index.qmd` is empty, I would get an error during rendering if I would remove it. However, with file `index.qmd` comes automagically an additional chapter that is unwanted and in my opinion not useful at all.
Any idea how to unset the additional chapter?
Help is appreciated!
</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-09-22T14:38:57Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement",
"books"
],
"locked": false,
"milestone": "v1.4",
"number": 2556,
"state": "open",
"title": "Add Support for Books With No `index.qmd` File",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2556"
} |
### Bug description
Example document:
```
---
title: "Test"
format:
html:
theme: cosmo
pdf:
indent: true
keep-tex: true
---
1. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam tempus iaculis
interdum.
```{r fig-test}
#| echo: false
#| fig-cap: Ducks.
library(ggplot2)
ggplot(cars, aes(x = speed, y = dist)) +
geom_point()
```
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam tempus iaculis
interdum.
2. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nam tempus iaculis
interdum.
```
When rendered, the chunk appears incorrectly and without its caption:
However, if I make the code block indented by three spaces instead of four, the figure renders perfectly with its caption and numbering.
This seems to only affect the code chunk -- the subsequent sentence renders just fine. Perhaps with four-space indentation the output is incorrectly being treated as verbatim code? But it's not displayed in a verbatim block, so I don't know.
This is on macOS, with:
```
$ quarto --version
1.1.251
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-22T14:28:54Z",
"creator": "capnrefsmmat",
"is_pull_request": false,
"labels": [
"invalid"
],
"locked": false,
"milestone": null,
"number": 2555,
"state": "closed",
"title": "Code blocks inside lists mis-rendered, depending on indentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2555"
} |
### Bug description
Hi there,
I just figured out that if you want to render a PDF with documentclass `moderncv` you need to comment-out these lines in the latex-template:
```
% % Allow footnotes in longtable head/foot
% \IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
% \makesavenoteenv{longtable}
```
If you do not, you will get the error message
`undefined control sequence \begin{document}`
....just sayin... took me a while to find out... ;)
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-22T13:53:22Z",
"creator": "produnis",
"is_pull_request": false,
"labels": [
"enhancement",
"third-party"
],
"locked": false,
"milestone": null,
"number": 2553,
"state": "closed",
"title": "documentclass moderncv needs \"footnotes in longtable\" to be disabled",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2553"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2546
<div type='discussions-op-text'>
<sup>Originally posted by **werkstattcodes** September 22, 2022</sup>
I would like to number my figures without any additional caption text, just Figure 1, Figure 2...
When I use e.g.
```
#| fig-cap: ""
#| label: fig-chapter_d
```
I obtain e.g. `Figure 1: ?(caption)` as a result. I get the same result also when skipping the fig-cap row entirely from the chunk options. Is there any way to get the desired result?
Many thanks.
</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-09-22T13:23:38Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2551,
"state": "open",
"title": "Crossrefs: support uncaptioned floats",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2551"
} |
Visiting https://quarto.org/docs/get-started/ with a browser which the website identifies as running on Linux results in being shown a large button like object to click to "Download Quarto CLI 1.1.251 (Linux)" The link goes to a .deb package for x86.
Elsewhere on https://quarto.org/docs/get-started/ a .deb package for x86 is offered for download and is labelled as being for "Linux".
Many, popular, widely used, Linux distributions do not use .deb packages. As such .deb packages should not be labelled as being for "Linux" or prominently promoted to all Linux users as being what they need.
Popular, widely used, non-x86 Linux distributions exist, e.g. Raspberry Pi OS.
A better approach would be to offer the tarball by default for Linux users, clearly labelled as being for x86, and let people using x86 Linux distributions which do use .deb packages find and download the .deb if they want to.
| {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-22T10:52:02Z",
"creator": "mike-somethingnooneelsehasusedyet",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.2",
"number": 2550,
"state": "closed",
"title": ".deb package wrongly labelled as \"Linux\" and offered by default to Linux users",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2550"
} |
### Bug description
Currently, the default combination of background and foreground colors for inline code is below 4.5.
This is with the latest build of Quarto (from this git repo). I'm on a Mac, but I don't think that's relevant, as it's just about the HTML styling.
Live page of the qmd file is here <https://mara.quarto.pub/quarto-inline-code/>.
Here is the [`.qmd` source file](https://github.com/batpigandme/quarto-inline-code/blob/main/quarto-inline-code.qmd) (the contents of which are also shown below).
````
---
title: "quarto-inline-code"
format: html
---
Here is an example of `code` inline.
The color I'm getting for the inline code with no styling added is `#9954bb`.
The default background color for inline code is `#f6f6f6`.
The contrast ratio for these two is 4.47 (too low).
I can make this [WCAG compliant](https://www.w3.org/TR/WCAG20/#visual-audio-contrast-contrast) (CCR >= 4.5 for body text) by increasing the contrast by setting `$code-color` to `#9753b8`, but it would be nice if this was the default behavior.
Here is the [GitHub repo with code for this page](https://github.com/batpigandme/quarto-inline-code).
````
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 0,
"created_at": "2022-09-22T10:12:31Z",
"creator": "batpigandme",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2548,
"state": "closed",
"title": "Failing color contrast for default inline code styling for HTML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2548"
} |
### Bug description
`header-includes` is not explicitely documented, although it is used on https://quarto.org/docs/reference/formats/pdf.html . It is also wrongly mentioned on https://quarto.org/docs/output-formats/pdf-basics.html (the actual code uses `include-in-header`).
Maybe `header-includes` is deprecated in favor of the `text:` subkey of `include-in-header`? Then is it possible to specifiy both include files and literal text?
My use case is that I specify a `preamble.tex` file with `include-in-header`, but I also need to add an extra header line that doesn't belong in the preamble file (the preamble is generic while the one-line fix is specific to this project). It's possible but a bit messy to make another `.tex` file just for the one-line fix, and if I already give a `preamble.tex` file to `include-in-header` then I don't think I can use the `text:` subkey.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 10,
"created_at": "2022-09-22T10:03:47Z",
"creator": "knuesel",
"is_pull_request": false,
"labels": [
"documentation",
"enhancement"
],
"locked": false,
"milestone": "v1.2",
"number": 2547,
"state": "closed",
"title": "include-in-header / header-includes confusion",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2547"
} |
### Bug description
The `monofont` setting is ignored when rendering the following with quarto 1.1.251 (on Pop!_OS 22.04):
---
monofont: Iosevka
format:
beamer:
theme: metropolis
keep-tex: true
---
# Title
```
Some code
```
The setting works when rendering to pdf (`--to pdf`) instead of Beamer slides. It also works when rendering Beamer slides without `theme: metropolis`.
I think the problem is in this part of the template:
```
\ifPDFTeX
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
\usepackage{unicode-math}
\defaultfontfeatures{Scale=MatchLowercase}
\defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
\setmonofont[]{Iosevka}
\fi
\usetheme[]{metropolis}
```
Here the `\setmonofont[]{Iosevka}` line has no effect because the metropolis theme later calls `\setmonofont` again.
I can work around this problem by adding the following in the YAML header:
```
include-in-header:
text: \setmonofont{Iosevka}
```
The meteropolis theme also calls `\setsansfont` so probably the `sansfont` setting is similarly ignored.
Looking at the other beamer themes in my texlive installation, I found one other that also overwrites font settings: the "Saint Petersburg" theme. This one also calls `\setmainfont`, so I guess the `mainfont` setting would also not work with this theme.
Minor side issue: the `theme` setting is not documented on https://quarto.org/docs/reference/formats/presentations/beamer.html (it is documented on https://quarto.org/docs/presentations/beamer.html however).
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 10,
"created_at": "2022-09-22T09:34:53Z",
"creator": "knuesel",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": "v1.3",
"number": 2545,
"state": "closed",
"title": "monofont ignored with metropolis beamer theme",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2545"
} |
### Bug description
I have the following information in my `_quarto.yml`:
But when you go to my website: https://www.tabularmusings.com/, you can see that the twitter-card site information is not rendered in the header:
I checked another quarto blog (https://www.fast.ai/) and their site information also doesn't appear in the header.
Twitter card validator fails to render a card for either of the blogs as `twitter:site` is [a required piece of metadata](https://developer.twitter.com/en/docs/twitter-for-websites/cards/overview/markup).
Including my full `_quarto.yml` per instructions below:
```
project:
type: website
website:
title: "tabularmusings"
site-url: "https://www.tabularmusings.com"
navbar:
right:
- about.qmd
- icon: twitter
href: https://twitter.com/radekosmulski
- icon: github
href: https://github.com/radekosmulski
twitter-card:
site: "@radekosmulski"
creator: "@radekosmulski"
open-graph: true
format:
html:
theme: cosmo
css: styles.css
execute:
freeze: true
```
I am not using RStudio. I am using the following version of quarto: 1.1.189. I am deploying on netlify using the quarto plugin.
This is my OS version: Ubuntu 22.04.1 LTS
Thank you for your help! 🙂
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-22T05:01:13Z",
"creator": "radekosmulski",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2544,
"state": "closed",
"title": "twitter-card doesn't render `twitter:site` metadata which prevents cards from being rendered on Twitter",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2544"
} |
### Bug description
Hi, I am hitting this error, trying to render a .qmd file, using Quarto in PowerShell (same with VSCode) on Windows 10. I can use the julia-1.7 kernel in jupyter lab, no probs. And I can render a .qmd using the python3 kernel in quarto
```
Starting julia-1.7 kernel...Traceback (most recent call last):
File "C:\Program Files\Quarto\share\jupyter\jupyter.py", line 21, in <module>
from notebook import notebook_execute, RestartKernel
File "C:\Program Files\Quarto\share\jupyter\notebook.py", line 17, in <module>
from nbclient import NotebookClient
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\nbclient\__init__.py", line 6, in <module>
from .client import NotebookClient, execute # noqa: F401
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\nbclient\client.py", line 14, in <module>
from jupyter_client import KernelManager
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\jupyter_client\__init__.py", line 6, in <module>
from .asynchronous import AsyncKernelClient # noqa
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\jupyter_client\asynchronous\__init__.py", line 1, in <module>
from .client import AsyncKernelClient # noqa
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\jupyter_client\asynchronous\client.py", line 6, in <module>
from jupyter_client.channels import HBChannel
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\jupyter_client\channels.py", line 12, in <module>
import zmq.asyncio
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\zmq\__init__.py", line 103, in <module>
from zmq import backend
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\zmq\backend\__init__.py", line 31, in <module>
raise original_error from None
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\zmq\backend\__init__.py", line 26, in <module>
_ns = select_backend(first)
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\zmq\backend\select.py", line 31, in select_backend
mod = import_module(name)
File "C:\Users\arn203\.julia\conda\3\lib\importlib\__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "C:\Users\arn203\.julia\conda\3\lib\site-packages\zmq\backend\cython\__init__.py", line 6, in <module>
from . import (
ImportError: DLL load failed while importing _device: The specified module could not be found.
```
I'm pretty lost with this at this point! Any help would be much appreciated.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 32,
"created_at": "2022-09-21T19:44:40Z",
"creator": "EvoArt",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2539,
"state": "closed",
"title": "Cannot render preview with Julia Kernel",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2539"
} |
### Bug description
This **may be** related to #2466, or may be not... I can't seem to make the hybrid sidebar work. The site [here](https://github.com/giabaio/reprex-site) contains a few pages/folders. I have (successfully) setup a navigation bar and would like to add a sidebar for two of the other folders (`research` and `book`). I can't seem to make it appear on the research page/folder --- while it does work on the book page/folder.
Am I missing something obvious here?
Thanks!
Gianluca
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-21T16:28:42Z",
"creator": "giabaio",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2536,
"state": "closed",
"title": "Hybrid sidebar not working?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2536"
} |
### Bug description
This seems somewhat similar to #2388 but that was fixed in https://github.com/quarto-dev/quarto-cli/commit/335608f88e00721388c25534d1939a9e6889a406.
Here is a reprex using:
```bash
quarto-testing quarto --version
1.1.251
```
````md
---
title: "Untitled"
execute:
eval: true
echo: false
warning: false
format:
html:
toc: true
toc-location: left
page-layout: full
---
```{r r-pkgs}
library(dplyr)
library(glue)
library(gt)
library(purrr)
```
# Tables
::: {.panel-tabset}
```{r}
#| output: asis
res <- purrr::map_chr(unique(starwars$homeworld), \(hw) {
knitr::knit_child(text = c(
"## `r hw`",
"",
"```{r}",
"#| echo: false",
"starwars %>%",
" filter(homeworld == hw) %>%",
" count(sex) %>%",
" head() %>%",
" gt()",
"```",
"",
""
), envir = environment(), quiet = TRUE)
})
cat(res, sep = '\n')
```
:::
````
This appears to be some combination of `toc-location` and `page-layout` as mentioned [here](https://github.com/quarto-dev/quarto-cli/discussions/2173#discussioncomment-3612281). Here is a breakdown of those combinations:
| toc-location | page-layout | clickable_tabs |
|--------------|-------------|----------------|
| left | full | no |
| right | full | yes |
| left | NULL | yes |
| right | NULL | yes |
I can reproduce in RStudio (2022.07.1) and vscode (version 1.71).
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 3,
"created_at": "2022-09-21T15:43:22Z",
"creator": "boshek",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2533,
"state": "closed",
"title": "toc-location: left, page-layout: full result in tabs not being clickable",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2533"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2490
<div type='discussions-op-text'>
<sup>Originally posted by **kortdriessen** September 18, 2022</sup>
Hello,
Thanks for all of the fantastic work here, quarto is great.
I have two closely related questions:
1. Is there a way to manually set the text color for figure captions and quotes separately without changing the 'fontcolor' html format option within the quarto yaml options? It seems that this text color defaults to some transformation on the main fontcolor specification, but I'd like to set them independently of that if possible, just haven't been able to figure out where.
2. I cannot figure out any way at all to change the color for the TOC 'outline bar' or the quote outline marking... I cannot find anything in the html format options on quarto, or any way to change my scss theme, or any sass variable to let me manually set these colors, which seem to be specified as the same (I think). I've attached an image detailing exactly what I'm referring to if this doesn't make sense.
Thanks again for the great stuff, let me know if I can clarify!
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-21T00:58:02Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2524,
"state": "closed",
"title": "Create variable to theme the toc 'stripe' border for inactive TOC elements",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2524"
} |
### Bug description
In derivatives of `format: html` including `format: revealjs` if a `<hr>` tag is used within fences (matched pairs of `:::`) the fence breaks.
```
Using the hr tag inside of ::: causes issues
::: {.fragment}
<hr>
Example
:::
```
<img width="1075" alt="image" src="https://user-images.githubusercontent.com/9363263/191277982-aab6191a-d207-4055-a147-573a0b198670.png">
However, if we use explicit divs everything is fine:
```
But if we use explicit div tags things work
<div class="fragment">
<hr>
Example
```
<img width="1075" alt="image" src="https://user-images.githubusercontent.com/9363263/191278323-93ae9319-6f52-4253-ac7a-bd4ecf985c99.png">
Here's an entire `.qmd` example
````
---
title: "Untitled"
format: revealjs
---
Using the hr tag inside of ::: causes issues
::: {.fragment}
<hr>
Example
:::
------
But if we use explicit div tags things work
<div class="fragment">
<hr>
Example
</div>
````
# About RStudio
RStudio
2022.07.0 Build 548
© 2009-2022 RStudio, PBC
"Spotted Wakerobin" Release (34ea3031, 2022-07-06) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_5_0) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-20T14:02:41Z",
"creator": "charliejhadley",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 2519,
"state": "closed",
"title": "<hr> inside of fenced divs breaks the fence",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2519"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2512
<div type='discussions-op-text'>
<sup>Originally posted by **iusgit** September 20, 2022</sup>
Hi,
first thanks for this wonderful tool!
I created a book project and one output format is a docx (unfortunately... I'm not a friend of this, but the project commands it).
My book looks like this:
```
book:
chapters:
- index.qmd
- content/Chapter_01.qmd
- content/Chapter_02.qmd
```
File `index.qmd` is empty, I would get an error during rendering if I would remove it. However, with file `index.qmd` comes automagically an additional chapter that is unwanted and in my opinion not useful at all.
Any idea how to unset the additional chapter?
Help is appreciated!
</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-09-20T13:10:41Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2516,
"state": "closed",
"title": "Single File Books require `index.qmd`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2516"
} |
### Bug description
I am not able to disable the table of contents (TOC) for chapter 2 and onwards for the book output.
This is my `_quarto.yml` for testing.
```yml
project:
type: book
book:
chapters:
- index.qmd
- test.qmd
toc: false
```
This is `index.qmd`
````md
# Chapter
Lorem
## Section
Ipsum
````
And `test.qmd`
````md
# Next Chapter
Lorem
## Next Section
Ipsum
````
Even when I add
```yml
format:
html:
toc: false
```
to the top of `test.qmd`, I get a TOC in resulting `test.html`. Note that `index.html` respects the `toc` setting.
My OS is Windows. I have also verified that the issue persists in quarto-1.2.134
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 0,
"created_at": "2022-09-20T12:53:54Z",
"creator": "justanothergithubber",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2515,
"state": "closed",
"title": "Subsequent pages of book always have TOC",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2515"
} |
### Bug description
Adding a comment before the first slide adds an empty slide at the beginning.
This code correctly creates a single slide:
```rmd
---
format: revealjs
---
# Getting up
- Turn off alarm
- Get out of bed
```
This code generates an empty slide before the slide with content:
```rmd
---
format: revealjs
---
<!-- comment for myself -->
# Getting up
- Turn off alarm
- Get out of bed
```
I use `quarto-cli` 1.2.134 and RStudio 2022.07.1+554 on Windows 10.
Session info:
```r
> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.2.1 (2022-06-23 ucrt)
os Windows 10 x64 (build 19044)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Europe.utf8
ctype English_Europe.utf8
tz Europe/Paris
date 2022-09-20
rstudio 2022.07.1+554 Spotted Wakerobin (desktop)
pandoc 2.18 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cli 3.4.0 2022-09-08 [1] CRAN (R 4.2.1)
digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0)
evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.1)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.1)
jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0)
knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
lifecycle 1.0.2 2022-09-09 [1] CRAN (R 4.2.1)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0)
R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.1)
R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.2.0)
rlang 1.0.5 2022-08-31 [1] CRAN (R 4.2.1)
rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.1)
roxygen2 7.2.1 2022-07-18 [1] CRAN (R 4.2.1)
rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
rvest 1.0.3 2022-08-19 [1] CRAN (R 4.2.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
shrtcts 0.1.2 2022-04-29 [1] Github (gadenbuie/shrtcts@12ef67f)
stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)
styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0)
xaringanExtra 0.7.0 2022-07-16 [1] CRAN (R 4.2.1)
xfun 0.33 2022-09-12 [1] CRAN (R 4.2.1)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
[1] C:/Users/etienne/AppData/Local/R/win-library/4.2
[2] C:/Users/etienne/AppData/Local/Programs/R/R-4.2.1/library
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2022-09-20T11:47:55Z",
"creator": "etiennebacher",
"is_pull_request": false,
"labels": [
"bug",
"wontfix"
],
"locked": false,
"milestone": null,
"number": 2514,
"state": "closed",
"title": "Revealjs: adding a comment before the first slide adds an empty slide",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2514"
} |
### Bug description
Consider the test.ipynb jupyter file as:
```
#%%
import pandas as pd
x = pd.DataFrame({"a": [1.1, 2, 3], "b": [4, 5, 6]})
x
#%%
x.style.format('{:.0f}')
```
In jupyterlab, exporting as html has this as result.
:
By running `quarto render test.ipynb --to html`, the first table is properly formatted, but the second, which comes from the style method, is broken:
Jupyter lab version: 3.4.4
nbconvert version: 6.5.0
Ubuntu 22.04.1 LTS
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-09-20T11:40:17Z",
"creator": "a0th",
"is_pull_request": false,
"labels": [
"bug",
"third-party"
],
"locked": false,
"milestone": "Future",
"number": 2513,
"state": "open",
"title": "Pandas .style not compatible with html reports",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2513"
} |
### Bug description
# Description
- Windows 11
- quarto-cli version 1.1.251
Anaconda I have installed it before, but I have uninstalled it and replaced it with miniconda. At the same time, I also set an environment variable for `Quarto_python`.But I still get a mistake in running Quarto Check. Output is as follows
```bash
❯ quarto check
[>] Checking Quarto installation......OK
Version: 1.1.251
Path: D:\Program Files\Quarto\bin
CodePage: 936
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.9.12 (Conda)
Path: D:/ProgramData/Miniconda3/Python.exe
Jupyter: 4.10.0
Kernels: base, micropython, python38364bitfc016c1517d34469ac97e72b9510044e, python3, d2l
(\) Checking Jupyter engine render....2022-09-20 13:14:09,015 - traitlets - ERROR - Failed to run command:
['D:\\ProgramData\\Anaconda3\\python.exe', '-m', 'ipykernel_launcher', '-f', 'C:\\Users\\Sky\\AppData\\Local\\Temp\\tmphxxkvr19.json']
PATH='C:\\Users\\Sky\\.oh-my-posh;D:\\ProgramData\\Miniconda3;D:\\ProgramData\\Miniconda3\\Library\\mingw-w64\\bin;D:\\ProgramData\\Miniconda3\\Library\\usr\\bin;D:\\ProgramData\\Miniconda3\\Library\\bin;D:\\ProgramData\\Miniconda3\\Scripts;D:\\ProgramData\\Miniconda3\\bin;D:\\ProgramData\\Miniconda3\\condabin;D:\\Program Files\\Quarto\\bin;D:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v11.6\\bin;D:\\Program Files\\NVIDIA GPU Computing Toolkit\\CUDA\\v11.6\\libnvvp;C:\\Program Files\\Common Files\\Siemens\\Automation\\Simatic OAM\\bin;D:\\Program Files\\SMV6;D:\\Program Files\\Cfast;D:\\Program Files\\Python\\Python39\\Scripts;D:\\Program Files\\Python\\Python39;C:\\Program Files (x86)\\Common Files\\Intel\\Shared Libraries\\redist\\intel64\\compiler;C:\\Program Files\\Common Files\\Oracle\\Java\\javapath;C:\\Program Files (x86)\\Common Files\\Oracle\\Java\\javapath;C:\\Windows\\system32;C:\\Windows;C:\\Windows\\System32\\Wbem;C:\\Windows\\System32\\WindowsPowerShell\\v1.0;C:\\Windows\\System32\\OpenSSH;C:\\Program Files (x86)\\NVIDIA Corporation\\PhysX\\Common;C:\\Program Files\\NVIDIA Corporation\\NVIDIA NvDLISR;D:\\Program Files\\Microsoft VS Code\\bin;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0;C:\\WINDOWS\\System32\\OpenSSH;D:\\Program Files\\mingw64\\bin;C:\\Program Files\\dotnet;D:\\Program Files\\MATLAB\\R2016b\\runtime\\win64;D:\\Program Files\\MATLAB\\R2016b\\bin;D:\\Program Files\\MATLAB\\R2016b\\polyspace\\bin;D:\\Program Files\\MiKTeX\\miktex\\bin\\x64;D:\\Program Files\\Java\\jdk-15.0.2\\bin;E:\\AppData\\Android\\Sdk\\platform-tools;D:\\Program Files (x86)\\PDFtk Server\\bin;D:\\Applications\\firemodels\\FDS6\\bin;D:\\Program Files (x86)\\NIST\\CONTAM 3.4.0.2;D:\\Applications\\Scoop\\apps\\msys2-cn\\20210725\\usr\\bin;C:\\Program Files\\Microsoft SQL Server\\150\\Tools\\Binn;C:\\Program Files\\PKWARE\\pkzipc;D:\\Program Files\\LINGO 12;C:\\Program Files\\NVIDIA Corporation\\Nsight Compute 2022.1.0;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0;C:\\WINDOWS\\System32\\OpenSSH;D:\\Program Files (x86)\\WinSCP;C:\\amp\\Apache24\\bin;C:\\amp\\Apache24;C:\\amp\\php;C:\\amp\\MariaDB\\bin;C:\\ProgramData\\ComposerSetup\\bin;C:\\Users\\Sky\\scoop\\shims;D:\\Applications\\Scoop\\shims;D:\\Program Files\\Quarto\\bin;D:\\ProgramData\\Python\\Python310\\Scripts;D:\\ProgramData\\Python\\Python310;C:\\Users\\Sky\\AppData\\Local\\Programs\\Python\\Launcher;C:\\Users\\Sky\\AppData\\Roaming\\Aria2\\maria2c.exe;C:\\Users\\Sky\\.dotnet\\tools'
with kwargs:
{'stdin': -1, 'stdout': None, 'stderr': None, 'cwd': None, 'close_fds': False}
2022-09-20 13:14:09,015 - traitlets - ERROR - [WinError 2] The system cannot find the file specified
Traceback (most recent call last):
File "D:\ProgramData\Miniconda3\lib\site-packages\jupyter_client\manager.py", line 75, in wrapper
out = await method(self, *args, **kwargs)
File "D:\ProgramData\Miniconda3\lib\site-packages\jupyter_client\manager.py", line 389, in _async_start_kernel
await ensure_async(self._launch_kernel(kernel_cmd, **kw))
File "D:\ProgramData\Miniconda3\lib\site-packages\jupyter_client\utils.py", line 38, in ensure_async
return await obj
File "D:\ProgramData\Miniconda3\lib\site-packages\jupyter_client\manager.py", line 307, in _async_launch_kernel
connection_info = await self.provisioner.launch_kernel(kernel_cmd, **kw)
File "D:\ProgramData\Miniconda3\lib\site-packages\jupyter_client\provisioning\local_provisioner.py", line 204, in launch_kernel
self.process = launch_kernel(cmd, **scrubbed_kwargs)
File "D:\ProgramData\Miniconda3\lib\site-packages\jupyter_client\launcher.py", line 170, in launch_kernel
raise ex
File "D:\ProgramData\Miniconda3\lib\site-packages\jupyter_client\launcher.py", line 158, in launch_kernel
proc = Popen(cmd, **kwargs)
File "D:\ProgramData\Miniconda3\lib\subprocess.py", line 951, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
File "D:\ProgramData\Miniconda3\lib\subprocess.py", line 1420, in _execute_child
hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] The system cannot find the file specified
[WinError 2] The system cannot find the file specified
[>] Checking Jupyter engine render....OK
```
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 10,
"created_at": "2022-09-20T05:29:02Z",
"creator": "Dagwbl",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": null,
"number": 2510,
"state": "closed",
"title": "Error: Checking Jupyter engine render",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2510"
} |
Hi, sorry if I misunderstood this.
When I use OJS to make slides interactive, it is only interactive while running on the local server.
However, if I open the generated `html` file directly in the browser, the interactive bars do not show up.
Maybe I'm missing something, or this is the expected behaviour. If the former, I apologize.
If the latter, I'd suggest a modification to the following part of the [documentation](https://quarto.org/docs/interactive/):
> One benefit of using JavaScript for interactive documents is that all the logic and computation is performed on the client (so no server is required for deployment).
Reproducible Example:
````
---
title: "Reproducible Example "
format: revealjs
editor: visual
---
## Home
```{ojs}
viewof size_bar = {
let input = Inputs.range([50, 150],
{value: 70,
step: 1,
label: "Size Bar: "});
return input;
}
```
````
| {
"assignee": null,
"comments": 4,
"created_at": "2022-09-20T00:43:05Z",
"creator": "Lourenzutti",
"is_pull_request": false,
"labels": [
"invalid"
],
"locked": false,
"milestone": null,
"number": 2529,
"state": "closed",
"title": "OJS - not locally interactive",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2529"
} |
### Bug description
Having a code chunk that uses `output-location` which is then wrapped by a fenced div causes the rendered document to fail back to the default output location.
See the following reprex below, it is expected that output should appear next to the code but it appears below. If the `::: {.test}` fenced div is removed then the document renders as expected. This failure occurs for any of the possible values of `output-location`.
````md
---
format: revealjs
---
```{r include=FALSE}
library(tidyverse)
```
## Code
::: {.test}
```{r}
#| echo: true
#| output-location: column
(d = tibble::tribble(
~country, ~"1999", ~"2000",
"A", "0.7K", "2K",
"B", "37K", "80K",
"C", "212K", "213K"
))
```
:::
````
RStudio 2022.07.1 Build 554
Quatro versions: bundled (1.0.36), latest (1.1.251), dev (1.2.126)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "jjallaire",
"comments": 0,
"created_at": "2022-09-19T16:05:37Z",
"creator": "rundel",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.2",
"number": 2503,
"state": "closed",
"title": "Fenced divs break output-location for revealjs documents",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2503"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/2498
<div type='discussions-op-text'>
<sup>Originally posted by **cbrnr** September 19, 2022</sup>
I have a website project and I'm trying to set the default engine to `knitr`. I tried adding this to my `_quarto.yml`:
```
engine:
knitr
```
However, this doesn't seem to have any effect, because all of my sub-documents still use the Jupyter engine.</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-09-19T15:56:44Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"yaml-validation"
],
"locked": false,
"milestone": "v1.2",
"number": 2502,
"state": "closed",
"title": "YAML parse bug",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2502"
} |
Not tagging this as a bug as I'm not sure if I'm doing something wrong -- would appreciate any help. I'm using Quarto 1.1.251.
Inputs in ObservableJS cells created in Quarto with hugo as the output format, then rendered to html using hugo seem to be hidden. Here is an example qmd:
````
---
title: Test Quarto + Hugo + OJS
author: Aaron Schiff
date: 2022-09-19T17:12:56+12:00
draft: false
format: html
execute:
echo: false
warning: true
---
## Testing OJS input
```{ojs}
viewof test_input = Inputs.select(['A', 'B', 'C'], { label: "Pick one:" });
```
Should be input box above here.
````
The output after rendering with hugo looks like this:
<img width="775" alt="Screen Shot 2022-09-19 at 17 26 48" src="https://user-images.githubusercontent.com/10150126/190954454-77a9b049-0686-4456-a3db-918c81c5b629.png">
The select input exists in the rendered html but has `display: none;` applied by `quarto-ojs.css`:
<img width="1136" alt="Screen Shot 2022-09-19 at 17 29 07" src="https://user-images.githubusercontent.com/10150126/190954996-bff0e674-1489-439c-b8d4-dbadb031e8c6.png">
If I change the output target to html, the select input appears as expected:
<img width="464" alt="Screen Shot 2022-09-19 at 17 33 18" src="https://user-images.githubusercontent.com/10150126/190954974-8056e88a-c94c-4d3f-9624-9fb2799bf174.png">
Is this a Quarto issue or have I done something wrong, eg in the yaml? | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-09-19T05:38:56Z",
"creator": "aaronschiff",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "Future",
"number": 2495,
"state": "open",
"title": "OJS inputs hidden in Hugo output?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2495"
} |
### Bug description
Consider the following minimal working example
``````
---
title: "MWE"
format:
docx: default
---
Some text
```{r}
#| echo: false
#| label: tbl-foo
#| tbl-cap: Some table
iris |>
head() |>
knitr::kable()
```
```{r}
#| echo: false
#| label: fig-bar
#| fig-cap: Mininal data visualisation.
plot(iris$Petal.Length, iris$Petal.Width)
```
``````
It produces
Please note that the figure is part of the table. This is more clear when the table spans two pages:
The expected behaviour was
where the figure outside the table.
## System Information
```
$ uname -srv
Linux 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022
$ quarto check
[✓] Checking Quarto installation......OK
Version: 1.2.131
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[✓] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /opt/conda/lib/R/library
rmarkdown: 2.16
[✓] Checking Knitr engine render......OK
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-19T02:30:58Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug",
"pandoc-lua"
],
"locked": false,
"milestone": "v1.2",
"number": 2493,
"state": "closed",
"title": "Figure concatenated to previous table in DOCX",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2493"
} |
### Bug description
Consider the following minimal working example
```
---
title: "MWE"
format:
pdf:
documentclass: article
pdf-engine: xelatex
keep-tex: true
---
Figures
::: {#fig-elephants layout-ncol="2"}
Famous Elephants
:::
````
It produces
Note that the subfigures are label as normal figures. The LaTeX produced by Quarto is
```
\begin{figure}
\begin{minipage}[t]{0.50\linewidth}
{\centering
\raisebox{-\height}{
\includegraphics{elephant.png}
}
\caption{Surus}
}
\end{minipage}%
%
\begin{minipage}[t]{0.50\linewidth}
{\centering
\raisebox{-\height}{
\includegraphics{elephant.png}
}
\caption{Hanno}
}
\end{minipage}%
\caption{\label{fig-elephants}Famous Elephants}
\end{figure}
```
Now compare the minimal working example with a patched version of it that has cross reference information.
```
---
title: "MWE"
format:
pdf:
documentclass: article
pdf-engine: xelatex
keep-tex: true
---
Figures
::: {#fig-elephants layout-ncol="2"}
{#fig-surus}
{#fig-hanno}
Famous Elephants
:::
```
It produces
Note that the subfigures are label properly. The LaTeX produced by Quarto is
```
\begin{figure}
\begin{minipage}[t]{0.50\linewidth}
{\centering
\raisebox{-\height}{
\includegraphics{elephant.png}
}
}
\subcaption{\label{fig-surus}Surus}
\end{minipage}%
%
\begin{minipage}[t]{0.50\linewidth}
{\centering
\raisebox{-\height}{
\includegraphics{elephant.png}
}
}
\subcaption{\label{fig-hanno}Hanno}
\end{minipage}%
\caption{\label{fig-elephants}Famous Elephants}
\end{figure}
```
Would be great if Quarto can generate a cross reference information for the subfigures so that users avoid experience the issue reported in the minimal working example.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-09-19T02:13:00Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 2492,
"state": "open",
"title": "Float crossrefs with unlabeled subfloats",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2492"
} |
### Bug description
Hi all,
I'm trying to include some emojis in a pdf document. The following code just yields white spaces where the emojis should be:
`--- from: markdown+emoji format: pdf pdf-engine: lualatex --- :house: :telephone_receiver:`
I've tried a few different pdf-engines and stuff. HTML works fine. Using the following RStudio on Mac OS 12.5.1.
RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 12_5_1) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
Regards,
Matt
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-19T01:08:30Z",
"creator": "mhollanders",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2491,
"state": "closed",
"title": "Emojis don't show up in pdf",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2491"
} |
### Bug description
Here is a sample document:
```qmd
---
title: "German Example"
date: 2022-09-18
lang: de
author: "Author Name"
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
```
When compiled with quarto (recent main branch, commit 30df30b5) the header includes:
```html
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Authors</div>
<div class="quarto-title-meta-contents">
<p>Author Name </p>
</div>
</div>
<div>
<div class="quarto-title-meta-heading">Veröffentlichungsdatum</div>
<div class="quarto-title-meta-contents">
<p class="date">18. September 2022</p>
</div>
</div>
</div>
```
Note that the heading for the date has been localized (into "Veröffentlichungsdatum"), the heading for the author has not (should be "Autor:innen").
Running on macOS Monterey.
### Checklist
- [x] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 0,
"created_at": "2022-09-18T16:09:21Z",
"creator": "jkseppan",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2485,
"state": "closed",
"title": "The \"authors\" part of the title does not get localized",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2485"
} |
### Bug description
Everything is right on the visual editor before rendering the pdf document, but I got the above error.
I am writing the formulas as follows:
`$Hd_2 = H d_1 * \left[\frac{ ( 1 - e ^ {\beta_1Id_1} ) ^ { \beta_2} } { ( 1 - e ^ {\beta_2Id_2} ) } \right]$`
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-09-18T04:02:15Z",
"creator": "Gabrielforest",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "Future",
"number": 2481,
"state": "closed",
"title": "Error using LaTeX formulas in tables",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2481"
} |
### Bug description
Hello,
I publish my blog with Quarto. I am getting error with generated XML RSS feed:
```
This page contains the following errors:
error on line 8 at column 30: xmlParseEntityRef: no name
Below is a rendering of the page up to the first error.
```
[Here](https://github.com/mrtkp9993/MyDsProjects/blob/main/docs/index.xml) is the generated XML feed. Error didn't change whether if I build with Rstudio or Quarto CLI.
Quarto version: 1.2.90
RStudio version: 2022.07.1 Build 554
OS: Win 10 Pro Version 10.0.19044 Build 19044
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-09-17T18:53:44Z",
"creator": "mrtkp9993",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2479,
"state": "closed",
"title": "Generated feed error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2479"
} |
### Bug description
Reported by @hamelsmu. If you include the `ioynb` format in a website absolute image references are not resolved (and result in a pandoc error). The same documents rendered to `html` do not exhibit the error.
Here is a minimal example repo: https://github.com/hamelsmu/quarto_nbcopy
In this repo, the following markdown results in an error when doing a `quarto render` of the entire site (which will pickup the `ipynb` renders):
````markdown
---
author: [Hamel Husain, Jeremy Howard]
date: 2022-07-28
image: /images/card.png
description: Our favorite tool for software engineering productivity--nbdev, now re-written with Quarto
tags: [technical]
title: 'nbdev+Quarto: A new secret weapon for productivity'
---
_[Originally posted](https://www.fast.ai/2022/07/28/nbdev-v2/) on the fast.ai blog_
````
This version (where the image paths are made relative) does work correctly:
````markdown
---
author: [Hamel Husain, Jeremy Howard]
date: 2022-07-28
image: /images/card.png
description: Our favorite tool for software engineering productivity--nbdev, now re-written with Quarto
tags: [technical]
title: 'nbdev+Quarto: A new secret weapon for productivity'
---
_[Originally posted](https://www.fast.ai/2022/07/28/nbdev-v2/) on the fast.ai blog_
````
Note that the absolute image reference does work in both cases within the YAML (`image` option) but fails in the body.
I know that we are doing some resource resolution in Lua (which in theory should pick this up) but we also have some resolution happening in HTML post-processors (which won't be run for ipynb). My suspicion is that we might be over-relying on the post-processing here and we need to make sure this all happens in Lua.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-09-17T11:15:53Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2475,
"state": "closed",
"title": "absolute image refs don't work for ipynb output in websites",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2475"
} |
### Bug description
I saw this issue brought up in the mapview discussion [here](https://github.com/r-spatial/mapview/issues/419). But the mapshot function does not seem to be playing well with quarto. I am trying to render a quarto project to pdf and html. If I leave a leaflet map as-is and render then I get an image that looks like this:
I get the following error when I try correct this issue using mapshot with my leaflet map created.
Could not load c:%5CUsers%5Cericv%5CAppData%5CLocal%5CTemp%5CRtmpeixsB4%5Cfile46f0695b5cb1.html
Error in (function (url = NULL, file = "webshot.png", vwidth = 992, vheight = 744, :
webshot.js returned failure value: 1
Any help addressing this would be helpful in avoiding having to manually screenshot the map and save and then embed a png to the quarto doc!! See here: https://github.com/hdadvisors/chesterfield-market-analysis/blob/quarto-transition/part-1a-3.qmd#L121
I'm running on PC, Windows 11 Pro. Running 2022.07.1 Build 554
"Spotted Wakerobin" Release (7872775e, 2022-07-22) for Windows
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-09-16T21:50:07Z",
"creator": "ericvmai",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 2470,
"state": "closed",
"title": "Mapshot and quarto not playing together?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2470"
} |
The subscription box displays correctly on the index page:
<img width="327" alt="Screenshot 2022-09-16 at 16 43 01" src="https://user-images.githubusercontent.com/45441679/190677995-f35e1023-f4e9-45b9-90e7-da9cce95e823.png">
However, the file name which contains the code required to display the email subscription box shows on other pages:
<img width="572" alt="Screenshot 2022-09-16 at 16 43 32" src="https://user-images.githubusercontent.com/45441679/190678386-08bde02c-86bb-4824-98c4-a525ab263e5b.png">
The file is named `subscribe.html` and is at the root of my project:
<img width="167" alt="Screenshot 2022-09-16 at 16 45 45" src="https://user-images.githubusercontent.com/45441679/190678490-be26449e-ffb3-466e-ba64-bc2f42340c61.png">
And I have added the file name to `_quarto.yml`:
```
website:
margin-header: subscribe.html
```
As per the [docs](https://quarto.org/docs/websites/website-blog.html#subscriptions)
quarto version 1.1.189 | {
"assignee": null,
"comments": 3,
"created_at": "2022-09-16T15:51:22Z",
"creator": "rossheat",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2467,
"state": "closed",
"title": "Email subscription embed code file name displays on pages",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2467"
} |
### Bug description
Hi all,
I can provide more detailed reprex but I wonder whether this is something that has been explored and has a simple solution? In a nutshell, in a listing page, if I set `categories` to `false`, the pagination and filter box still appear on the page, but they are not clickable. The first page of the many that get created (because I set `page-size: 7`) are simply not shown.
When I set `categories` to `true`, then things work as expected; I can use the filter by clicking on the box and typing whatever I want and I can click on the numbers to navigate to the other group of items.
Is this an obvious bug?
Thanks
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 11,
"created_at": "2022-09-16T12:43:44Z",
"creator": "giabaio",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 2466,
"state": "closed",
"title": "Website: Pagination/filter not working when categories is set to false?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2466"
} |
### Bug description
For all user-facing length specifications, please refrain from supporting dimensionless numbers implied to be inches.
Do support numbers only when combined with explicit units of measurement, such as `10in`, `17cm`, or `150mm`.
(Including, but by no means limited to `page-width`, `fig-width`, `fig-height` …)
Please do follow the examples of TeX/LaTeX, pandoc, and pretty much every text processor (MS Word, LibreOffice, Pages, etc.) there is in this respect.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-16T09:07:00Z",
"creator": "njbart",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 2463,
"state": "open",
"title": "For all length specifications, use proper units of measurement",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2463"
} |
### Bug description
`quarto render xyz.qmd` will throw `Fatal javascript OOM in Reached heap limit` when a certain number of figures are added (in our case plotly graphs). In our case it was 26 figures and we get OOM.
```
<--- Last few GCs --->
[2027:0x55bc3354a960] 66765 ms: Mark-sweep 1591.0 (1625.9) -> 1587.9 (1622.4) MB, 7.6 / 0.0 ms (average mu = 0.989, current mu = 0.989) allocation failure; scavenge might not succeed
<--- JS stacktrace --->
#
# Fatal javascript OOM in Reached heap limit
#
/usr/local/bin/quarto: line 128: 2027 Trace/breakpoint trap (core dumped) "${QUARTO_DENO}" ${QUARTO_ACTION} ${QUARTO_DENO_OPTIONS} ${QUARTO_DENO_EXTRA_OPTIONS} "${QUARTO_IMPORT_ARGMAP}" "${QUARTO_TARGET}" "$@"
```
This is the config we have:
```
---
execute:
echo: false
jupyter: python3
format:
html:
toc: true
toc-depth: 4
toc-location: left
html-math-method: katex
font-family: Inter,sans-serif
smooth-scroll: true
citations-hover: false
footnotes-hover: false
code-fold: true
code-summary: "Show the code"
code-overflow: wrap
theme: cosmo
fontsize: 1.1em
linestretch: 1.7
---
```
I removed `self-contained` as discussed here: https://github.com/quarto-dev/quarto-cli/issues/1263
I appologise I do not have a reproducible example. I have tried different linux distos such as Amazon Linux 2 and Ubuntu 22.04. Any ideas on how I might resolve this? Thank you.
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 26,
"created_at": "2022-09-16T04:27:38Z",
"creator": "nadnerb",
"is_pull_request": false,
"labels": [
"bug",
"deno",
"triaged-to"
],
"locked": false,
"milestone": "v1.4",
"number": 2462,
"state": "open",
"title": "Fatal javascript OOM in Reached heap limit on render html",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2462"
} |
### Bug description
## Bug description
Importing `matplotlib.pyplot` leads to `No module named 'matplotlib_inline'` error.
## Details
`reprex.qmd` is essentially a single line: `import matplotlib.pyplot as plt`. I have no trouble running this when calling `python3` on the command line. (I needed to change extension to `.txt` to paste here.)
```
(base) igow@igow-z640:~/git/lda_play$ export QUARTO_PRINT_STACK=true
(base) igow@igow-z640:~/git/lda_play$ quarto render reprex.qmd
Starting python3 kernel...Done
Executing 'reprex.ipynb'
Cell 1/1...ERROR:
An error occurred while executing the following cell:
------------------
import matplotlib.pyplot as plt
------------------
---------------------------------------------------------------------------
ModuleNotFoundError Traceback (most recent call last)
<ipython-input-1-a0d2faabd9e9> in <module>
----> 1 import matplotlib.pyplot as plt
~/miniconda3/lib/python3.9/site-packages/matplotlib/pyplot.py in <module>
2334 dict.__setitem__(rcParams, "backend", rcsetup._auto_backend_sentinel)
2335 # Set up the backend.
-> 2336 switch_backend(rcParams["backend"])
2337
2338 # Just to be safe. Interactive mode can be turned on without
~/miniconda3/lib/python3.9/site-packages/matplotlib/pyplot.py in switch_backend(newbackend)
274 backend_name = cbook._backend_module_name(newbackend)
275
--> 276 class backend_mod(matplotlib.backend_bases._Backend):
277 locals().update(vars(importlib.import_module(backend_name)))
278
~/miniconda3/lib/python3.9/site-packages/matplotlib/pyplot.py in backend_mod()
275
276 class backend_mod(matplotlib.backend_bases._Backend):
--> 277 locals().update(vars(importlib.import_module(backend_name)))
278
279 required_framework = _get_required_interactive_framework(backend_mod)
~/miniconda3/lib/python3.9/importlib/__init__.py in import_module(name, package)
125 break
126 level += 1
--> 127 return _bootstrap._gcd_import(name[level:], package, level)
128
129
ModuleNotFoundError: No module named 'matplotlib_inline'
ModuleNotFoundError: No module named 'matplotlib_inline'
```
## Version information
```
(base) igow@igow-z640:~/git/lda_play$ quarto --version
1.1.245
(base) igow@igow-z640:~/git/lda_play$ cat /etc/os-release
PRETTY_NAME="Ubuntu 22.04.1 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.1 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy
```
[reprex.txt](https://github.com/quarto-dev/quarto-cli/files/9580234/reprex.txt)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-16T02:49:38Z",
"creator": "iangow",
"is_pull_request": false,
"labels": [
"upstream"
],
"locked": false,
"milestone": null,
"number": 2461,
"state": "closed",
"title": "Issue with matplotlib_inline",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2461"
} |
Dear Quarto team,
I want to use Quarto to create a book. I would like to have a book where chapters are built from several Qmd files (sections - as I will end up having too many chapters otherwise) and I have been unable to understand from the [documentation ](https://quarto.org/docs/books/book-structure.html)whether this is possible with Quarto (as it seems both Bookdown and Jupyter Book allow for this) and, if this is the case, what the YAML syntax would be. I have divided my books into several parts already, but this does not replace the flexibility offered by sections.
From the same documentation it also seems that it is possible to split sections in different pages, but again I am unable to understand how I can do this.
"If you have a book with several pages in a section or subsection, it is often convenient to offer the user the ability to navigate to the next page (or previous page) at the bottom of the page that they’ve just finished reading."
Could you kindly provide clarity on this? Thank you in advance for your support. | {
"assignee": null,
"comments": 1,
"created_at": "2022-09-15T22:09:28Z",
"creator": "Thaliehln",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3382,
"state": "closed",
"title": "Quarto book - split chapters in separate QMD files (sections)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3382"
} |
### Bug description
I wasn't completely sure if this was better suited for the cli repo or the R repo, but here we are. The `tidytable` package recently introduced dotless versions of functions in its dev version (e.g. `mutate.() -> mutate()`), with one of them being its own version of `base::ifelse()` that ultimately calls `data.table::fifelse()` under the hood. It seems the stricter type checking of `fifelse` isn't playing nicely with a function that's calling `knitr`'s plot hook functions. The below fails on both html and pdf rendering:
````
---
format: html
---
```{r}
data("mtcars")
# devtools::install_github("markfairbanks/tidytable")
library(tidytable)
plot(mtcars$mpg, mtcars$cyl)
```
````
```
processing file: plot_example.qmd
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
Quitting from lines 6-13 (plot_example.qmd)
Error in fifelse(condition, args$true, args$false, args$missing) :
'yes' is of type NULL but 'no' is of type character. Please make sure that both arguments have the same type.
Calls: .main ... run_hook_plot -> hook -> ifelse -> if_else -> fifelse
Execution halted
```
I haven't had the time to read through the rmd-related code super closely, but I *think* it may be coming from [line 162](quarto-dev/quarto-cli/blob/main/src/resources/rmd/execute.R#L162) of `execute.R` since that's the only `ifelse` I've come across so far that seems like it could return two different types.
For posterity and completeness' sake, both PCs I've tested this on are running Windows 10 with the 1.1.168 cli. Any dev version of `tidytable` after [this commit](https://www.github.com/markfairbanks/tidytable/commit/83b826060a126c1974d18c4646b6739fdbfdbedc) will produce the error. Finally, the error doesn't occur if knitting an .rmd with the same code as above.
```
quarto help
Usage: quarto
Version: 1.1.168
Description:
Quarto CLI
```
```
packageVersion("knitr")
1.39
```
In the meantime, I've been calling `conflicted::conflict_prefer("ifelse", "base")` to get around the issue.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [x] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 7,
"created_at": "2022-09-15T14:47:34Z",
"creator": "mattsams89",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 2454,
"state": "closed",
"title": "Fatal error while rendering plots when `base::ifelse()` is masked by a stricter R function",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2454"
} |
I believe this example is not working as reference is shown on hover and not in the margin
where the doc says
> As an example, when I cite Xie, Allaire, and Grolemund ([2018](https://quarto.org/docs/authoring/article-layout.html#ref-xie2018)), the citation bibliography entry itself will now appear in the margin.
Or maybe it is but far away below... in there: https://quarto.org/docs/authoring/article-layout.html#options-reference
| {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-09-15T09:44:10Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 2451,
"state": "closed",
"title": "Reference citation should be in the margin for this example",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2451"
} |
### Bug description
The small example at https://gitlab.com/raniere-phd/quarto-document-template (output in the screenshot above) produces the callout image in DOCX too small.
Small Quarto file: https://gitlab.com/raniere-phd/quarto-document-template/-/blob/main/inst/index.qmd
Render log: https://gitlab.com/raniere-phd/quarto-document-template/-/jobs/3032161518
Environment information
```
$ quarto check
[✓] Checking Quarto installation......OK
Version: 1.2.108
Path: /opt/quarto/bin
[✓] Checking basic markdown render....OK
[✓] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[✓] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /opt/conda/lib/R/library
rmarkdown: 2.16
[✓] Checking Knitr engine render......OK
$ quarto tools check
[✓] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.09
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-09-15T09:19:43Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.2",
"number": 2450,
"state": "closed",
"title": "Docx callout images don't scale properly when DPI is set",
"url": "https://github.com/quarto-dev/quarto-cli/issues/2450"
} |
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