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### Bug description
[Zip with minimal working example](https://github.com/quarto-dev/quarto-cli/files/10205325/3629-mwe.zip)
Consider the follow Quarto document
``````
---
title: "Minimal Working Example"
---
Foo
```{r}
#| echo: false
#| eval: false
#| output: true
#| label: tbl-mwe
#| tbl-cap: MWE.
data.frame(
x = c(1, 2),
y = c(1, 2)
)
```
Bar
``````
Convert it to DOCX with `quarto render --to html` produces
Note the `?(caption)` between `Foo` and `Bar` produced as the output of the cell block.
Convert the same document to HTML with `quarto render --to html` produces
The cell block does **NOT** produce any visible output.
Change `output: true` to `output: false` resolves the problem but would be great that `eval: false` implies `output: false` for DOCX as it does for HTML.
# User Environment
`quarto check`:
```
[β] Checking Quarto installation......OK
Version: 1.3.34
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.10 (Conda)
Path: /home/raniere/mambaforge/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/raniere/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.16
[β] 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": "cscheid",
"comments": 0,
"created_at": "2022-12-12T07:09:31Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug",
"crossref",
"docx"
],
"locked": false,
"milestone": "v1.4",
"number": 3629,
"state": "open",
"title": "?(caption) in DOCX when eval: false and output: true",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3629"
} |
### Bug description
I set-up a new website following the approach described [here](https://quarto.org/docs/publishing/netlify.html#github-action):
- Repo hosted on GitHub
- Site built by GitHub actions
- Computations ran locally with creation of a `_freeze` directory put under version control
- Site hosted on Netlify
All worked great until I created a reveal.js presentation in that site with Julia code.
GitHub actions failed with the following error in "Render and Publish":
```
ERROR: Jupyter kernel 'julia-1.8' not found.
```
Since the computations are supposed to happen locally in this workflow, I don't understand what is happening.
My `.github/workflows/publish.yml` matches the one shown in the doc and I followed the set of instructions literally. My `_freeze` is under vc and all changes in it are pushed to GitHub.
Thanks for the help.
---
OS: Arch Linux (6.0.11-arch1-1)
---
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 22,
"created_at": "2022-12-12T03:46:55Z",
"creator": "prosoitos",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3628,
"state": "open",
"title": "GitHub actions not using _freeze content and unable to publish locally rendered Julia computations",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3628"
} |
### Bug description
My Vegalite plots that I'm creating using Observable with Quarto initially dont show up when I set `width("container")`. Interestingly, they *do* appear when I hit <kbd>F12</kbd> and fire up the javascript console in the the browser. Here is a minimal example:
````
---
title: "Vegalite with OJS and Quarto"
format: html
---
```{ojs}
import {vl} from "@vega/vega-lite-api-v5"
vl.markPoint().data(vl.sequence(1, 10, 1).as("x"))
.encode(
vl.x().fieldQ("x"),
vl.y().fieldQ("x")
)
// this following line causes the issue
.width("container")
.render()
```
````
Here's how it looks in my browser. If I remove `.width("container")` the plot appears directly.
- Here's a web version to try out: https://ratnanil.github.io/minimal-ojs
- Here's the repo with the code: https://github.com/ratnanil/minimal-ojs
[Screencast from 10.12.2022 09:19:24.webm](https://user-images.githubusercontent.com/12532091/206841049-fa7b001c-1101-45bb-933f-43d3533feac5.webm)
I'm running RStudio 2022.07.1 Build 554 on Ubuntu 22.04
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-12-10T08:34:11Z",
"creator": "ratnanil",
"is_pull_request": false,
"labels": [
"bug",
"wontfix",
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 3622,
"state": "closed",
"title": "Plot does not show initially when setting .width(\"container\") when using OJS and Vegalite",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3622"
} |
Minimal repro:
````
---
title: "test graphviz"
---
```{ojs}
dot`graph G {
a [tooltip="Tooltip for a"]
b [tooltip="Tooltip for b"]
c [tooltip="Tooltip for c"]
d [tooltip="Tooltip for d"]
a -- b;
b -- c;
c -- d;
d -- a;
}`
```
```{dot}
graph G {
a [tooltip="Tooltip for a"]
b [tooltip="Tooltip for b"]
c [tooltip="Tooltip for c"]
d [tooltip="Tooltip for d"]
a -- b;
b -- c;
c -- d;
d -- a;
}
```
```` | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-12-08T23:18:24Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"ojs-engine"
],
"locked": false,
"milestone": "v1.4",
"number": 3612,
"state": "open",
"title": "Graphviz tooltips are rendered inconsistently from `dot` to `ojs`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3612"
} |
### Bug description
````
---
title: "missing caption causes crash"
format: html
---
```{r}
#| label: load_data
data(cars)
library(flextable)
```
Now lets try a table in our word document. This should be X.
```{r}
#| label: cars
cars |>
dplyr::slice_head(n = 5) |>
flextable() |>
autofit()
```
````
Output of `quarto::quarto_render("not_allowed_missing_caption.qmd", output_format = "html")`:
```
processing file: not_allowed_missing_caption.qmd
|.............. | 20%
ordinary text without R code
|............................ | 40%
label: load_data
|.......................................... | 60%
ordinary text without R code
|........................................................ | 80%
label: cars
Quitting from lines 17-22 (not_allowed_missing_caption.qmd)
Error in opts_current_table() :
if a label (cars) is defined, chunk option `tbl-cap` should also be defined.
Calls: .main ... flextable_to_rmd -> knit_to_html -> opts_current_table
Execution halted
Error in `processx::run(quarto_bin, args, echo = TRUE)`:
! System command 'quarto' failed
---
Exit status: 1
stdout & stderr: <printed>
---
```
Making the document an Rmd instead, and using `rmarkdown`, it works fine. So it's definitely something to do with `quarto`, even though we are using the `knitr` engine as it's R code.
Their are many reasons a user might not want table captions, not least because they've coded workarounds to #3600 and #3601 by [managing the referencing themselves](https://github.com/rmflight/documentNumbering), but now they can't use that approach (or even just not have captions at all if they so desire), because `quarto` is being extremely opinionated on there **having to be** captions included. And I shouldn't have to have it *unlabeled* either, because labels are useful regardless of whether they are being used for cross-referencing or not.
* R 4.2.1
* RStudio 2022.12.0-preview+348
* quarto 1.3.47
* Linux, Pop! OS 22.04 (skinned version of Ubuntu 22.04)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-12-08T16:45:55Z",
"creator": "rmflight",
"is_pull_request": false,
"labels": [
"bug",
"crossref",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 3603,
"state": "open",
"title": "error if no table caption included",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3603"
} |
In some situations, users might be running quarto with their own dependencies. Although we try to ship our own, sometimes that doesn't work out (consider alternative architectures, for example).
It would be nice if `quarto check` would run version checks of the dependencies so that if (eg) users are running an old version of Pandoc, we could issue a warning. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-12-08T16:42:04Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 3602,
"state": "closed",
"title": "Warn about old versions of binary dependencies",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3602"
} |
### Bug description
````
---
title: "flextable missing reference"
format: docx
---
```{r}
#| label: load_data
data(cars)
library(flextable)
```
Now lets try a table in our word document. This should be @tbl-cars.
```{r}
#| label: tbl-cars
#| tbl-cap: Something about cars.
cars |>
dplyr::slice_head(n = 5) |>
flextable() |>
autofit()
```
````
[flextable_missing.docx](https://github.com/quarto-dev/quarto-cli/files/10187485/flextable_missing.docx)
Rendering the above document (RStudio render button) results in the table reference looking like ?@tbl-cars, and there is no caption.
If I force HTML output (quarto::quarto_render(..., output_format = "html")), I get the expected output of Table 1, as well as the caption.
Software details:
* R 4.2.1
* RStudio 2022.12.0-preview+348
* quarto 1.3.47
* flextable 0.8.4.001 2022-12-08 davidgohel/flextable@f38ccb1
* Linux, Pop! OS 22.04 (skinned version of Ubuntu 22.04)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-12-08T16:35:21Z",
"creator": "rmflight",
"is_pull_request": false,
"labels": [
"bug",
"crossref",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 3601,
"state": "open",
"title": "missing reference for flextable table in word document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3601"
} |
### Bug description
````
---
title: "gt missing reference"
format: docx
---
```{r}
#| label: load_data
data(cars)
library(gt)
```
Now lets try a table in our word document. This should be @tbl-cars.
```{r}
#| label: tbl-cars
#| tbl-cap: Something about cars.
cars |>
dplyr::slice_head(n = 5) |>
gt()
```
````
[gt_missing_reference.docx](https://github.com/quarto-dev/quarto-cli/files/10187371/gt_missing_reference.docx)
Rendering the above document (RStudio render button) results in the table reference looking like `?@tbl-cars`, and there is no caption.
If I force HTML output (`quarto::quarto_render(..., output_format = "html")`), I get the expected output of `Table 1`, as well as the caption.
Software details:
* R 4.2.1
* RStudio 2022.12.0-preview+348
* quarto 1.3.47
* gt rstudio/gt@d638baa
* Linux, Pop! OS 22.04 (skinned version of Ubuntu 22.04)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-12-08T16:22:18Z",
"creator": "rmflight",
"is_pull_request": false,
"labels": [
"bug",
"crossref",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 3600,
"state": "open",
"title": "missing reference for gt table in word document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3600"
} |
@cderv, can you check if the hashes are computed differently on windows and unix? I suspect something is doing newline normalization on our code.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3597
<div type='discussions-op-text'>
<sup>Originally posted by **espinielli** December 8, 2022</sup>
Hi all,
I have set a CI workflow where Netlify published a quarto book as per [1] (we specifically use this for automatic preview on development branch [2][3]).
I am using the `freeze` option to get the code chunks pre-computed as required by the Netlify setup.
The issue is that pushes from the same source from different machine (mac and Windows) produce different hashes for the same qmd sources...and this means git merge clashes and difficulties to collaborate...
We use the same quarto version on the two OSs...
Here is an example of the clash:
```json
{
<<<<<<< HEAD
"hash": "3575a3f572f6cd1d1124f5223cdfb566",
=======
"hash": "ada4b65f5349f9aad31f8f739195a811",
>>>>>>> 67c67552f0aba0e2ab86d751957e6d3384296cc6
"result": {
"markdown": "\n# Welcome {-}\n\nThis is the website for __\"{{< meta title >}}\"__.\n\n\nThe EUROCONTROL Business Cases team regularly refreshes the content and the underlying data\nin order to provide up-to-date information for the interested users.\n\n\n# About us\n\nEUROCONTROL Business Cases team is a dedicated team of experts supporting stakeholders to choose among different solutions and alternatives making use of the best available data. For more than 15 years, EUROCONTROL has been providing ATM decision makers with a wide range of information enabling them to take rational long-term investment decisions.\n\n# Notice and Disclaimer {-}\n\nThe EUROCONTROL Business Cases team has made every effort to ensure that the information and analysis contained in this document are as accurate as possible. Only information from quoted sources has been used\nand information relating to named parties has been checked with the parties concerned. Despite these\nprecautions, should you find any errors or inconsistencies we would be grateful if you could please bring them to\nour attention. Our email address is [[email protected]](mailto:[email protected])\n\nThis document is published by the EUROCONTROL Business Cases team in the interest of the exchange of\ninformation.\n\nInformation contained in this document may not be modified without prior written permission from the\nEUROCONTROL Business Cases team.\n\nThe views expressed herein do not necessarily respect the official views or policy of EUROCONTROL, which\nmakes no warranty, either implied or express, for the information contained in this document, neither does it\nassume any legal liability or responsibility for the accuracy, completeness or usefulness of this information.\n\n\n\n\n## Publications {-}\n\n| EUROCONTROL Headquarters\n| 96 Rue de la FusΓ©e\n| B-1130 BRUSSELS\n| Tel: +32 (0)2 729 1152\n| Fax: +32 (0)2 729 5149\n| E-mail: [email protected]",
"supporting": [],
"filters": [
"rmarkdown/pagebreak.lua"
],
"includes": {},
"engineDependencies": {},
"preserve": {},
"postProcess": true
}
}
```
In a way it would be great to generate same hash from same source...
I initially thought this was due to line termination differences in the two OS architectures, so I forced line termination via `.gitattributes` to no avail unfortunately.
Has anybody had same/similar issues?
[1] <https://quarto.org/docs/publishing/netlify.html#rendering-on-netlify>
[2] <https://github.com/euctrl-pru/standard_inputs/pull/4>
[3] <https://deploy-preview-4--standard-inputs.netlify.app/></div> | {
"assignee": "cscheid",
"comments": 11,
"created_at": "2022-12-08T15:14:59Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": "v1.4",
"number": 3599,
"state": "open",
"title": "same source different hashes in _freeze/ files from different OS machines",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3599"
} |
Hi,
I have a problem rendering ggplot2 figures which include non-ascii/non-english characters, but only when the output is a pdf file. For example, this code:
``` r
library(ggplot2)
ggplot(mtcars, aes(x = am, y = mpg)) +
geom_jitter() +
labs(x = "PΕΓliΕ‘ ΕΎluΕ₯ouΔkΓ½ kΕ―Ε")
```
Returns following:
<img width="708" alt="quarto-pdf-latex" src="https://user-images.githubusercontent.com/61730945/206162433-9f66d07e-8c8b-48c0-924c-d6d86585a706.png">
I vaguely remember having the same problem with Rmarkdown some years ago, but then I managed to solve it by using AGG as graphical device (through the [ragg](https://ragg.r-lib.org) package). This however doesn't work with Quarto. (Unless I'm mistaken, Quarto doesn't even let you select graphical device).
The figures look perfect when exporting to docx or html. I'm using tinytex 0.42 as my latex distribution, as well as Rstudio 2022.07.2 Build 576.
Thanks for help!
``` r
sessioninfo::session_info()
#> β Session info βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
#> setting value
#> version R version 4.2.2 (2022-10-31)
#> os macOS Ventura 13.0
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Europe/Prague
#> date 2022-12-07
#> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
#>
#> β Packages βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
#> package * version date (UTC) lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.0)
#> colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
#> curl 4.3.3 2022-10-06 [1] CRAN (R 4.2.0)
#> DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
#> digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.0)
#> dplyr 1.0.10 2022-09-01 [1] CRAN (R 4.2.0)
#> evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.2)
#> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
#> farver 2.1.1 2022-07-06 [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)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
#> ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.2.2)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
#> gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0)
#> httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.0)
#> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.0)
#> labeling 0.4.2 2020-10-20 [1] CRAN (R 4.2.0)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
#> mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
#> purrr 0.3.5 2022-10-06 [1] CRAN (R 4.2.0)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0)
#> 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 2.12.2 2022-11-11 [1] CRAN (R 4.2.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
#> rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.2)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
#> scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0)
#> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.0)
#> styler 1.8.1 2022-11-07 [1] CRAN (R 4.2.0)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
#> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
#> vctrs 0.5.0 2022-10-22 [1] CRAN (R 4.2.0)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
#> xfun 0.34 2022-10-18 [1] CRAN (R 4.2.0)
#> xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
#> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.0)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
#>
#> ββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
``` | {
"assignee": null,
"comments": 1,
"created_at": "2022-12-07T11:19:17Z",
"creator": "alesvomacka",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3591,
"state": "closed",
"title": "Some non-english characters in ggplot2 figures are not rendered correctly when exporting to PDF",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3591"
} |
### Bug description
`quarto render --help` says
```
Usage: quarto render [input] [args...]
```
and `quarto render mwe.qmd --to docx` works as expected
```
pandoc
to: docx
output-file: mwe.docx
default-image-extension: png
metadata
title: Minimal Working Example
Output created: mwe.docx
```
Unfortunately, `quarto render --to docx mwe.qmd` produces a document with duplicated content (see https://github.com/quarto-dev/quarto-cli/issues/3579).
Will be possible to include a warning in the command line output if the input file is not the first argument?
`quarto check` reports
```
[β] Checking Quarto installation......OK
Version: 1.3.34
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.10 (Conda)
Path: /home/raniere/mambaforge/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/raniere/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.16
[β] 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": "cscheid",
"comments": 5,
"created_at": "2022-12-06T07:02:15Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3581,
"state": "closed",
"title": "Make command line robust against argument order",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3581"
} |
### Bug description
[Zip file with minimal working example](https://github.com/quarto-dev/quarto-cli/files/10163470/mwe.zip)
Consider the minimal working example with subfigures:
``````
---
title: "Minimal Working Example"
format: docx
---
Foo
::: {#fig-1 layout-ncol="2"}
{width="5cm"}
Logos
:::
Bar
``````
Render using `quarto render subfigure-height.qmd --to docx` produces
The figure is not 5cm width and overflows the available space.
For comparison, consider the minimal working example with single figure:
``````
---
title: "Minimal Working Example"
format: docx
---
Foo
{width="5cm"}
Bar
``````
Render using `quarto render figure-height.qmd --to docx` produces
The figure is 5cm width as instructed with `{width="5cm"}`.
`quarto check` reports
```
[β] Checking Quarto installation......OK
Version: 1.3.34
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.10 (Conda)
Path: /home/raniere/mambaforge/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/raniere/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.16
[β] 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": "cscheid",
"comments": 4,
"created_at": "2022-12-06T06:50:16Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"docx"
],
"locked": false,
"milestone": "v1.4",
"number": 3580,
"state": "closed",
"title": "Subfigures ignore width and height attributes ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3580"
} |
### Bug description
Consider the follow minimal working example
```
---
title: "Minimal Working Example"
format: docx
---
Foo
```
Render the above example using `quarto render --to docx duplication.qmd` produces
Note that `Foo` is duplicated.
`quarto check` reports
```
[β] Checking Quarto installation......OK
Version: 1.3.34
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.10 (Conda)
Path: /home/raniere/mambaforge/bin/python
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with conda install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/raniere/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.16
[β] 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": 2,
"created_at": "2022-12-06T06:24:27Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3579,
"state": "closed",
"title": "Document content duplicated when render to DOCX with quarto 1.3.34",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3579"
} |
Minimal repro:
````
---
title: "Test of Reveal.js"
format: revealjs
---
## Here is a slide
It's got some text on it.
::: {.content-visible when-format="html"}
## Title will only appear in HTML
:::
This text is confusing the machinery.
## Here is another slide
It's got some text on it too
```` | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-12-05T22:35:03Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 3575,
"state": "closed",
"title": "Conditional content confuses revealjs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3575"
} |
### Bug description
TLDR; CairoMakie figures render fine on first render. Subsequent renders produce empty figure-pdf files causing LaTeX compilation failures.
Consider the following example
````md
---
title: hello world
jupyter: julia-1.8
---
```{julia}
using CairoMakie
lines(-2..2, sin )
```
````
When you first call `quarto render main.qmd --to pdf` everything renders without issue with the following output
```
Starting julia-1.8 kernel...Done
Executing 'main.ipynb'
Cell 1/1...Done
pandoc
to: latex
output-file: main.tex
standalone: true
pdf-engine: xelatex
variables:
graphics: true
tables: true
default-image-extension: pdf
metadata
documentclass: scrartcl
classoption:
- DIV=11
- numbers=noendperiod
papersize: letter
header-includes:
- '\KOMAoption{captions}{tableheading}'
block-headings: true
title: hello world
jupyter: julia-1.8
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
running xelatex - 2
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
Output created: main.pdf
```
However if you call the same render command again I get
```
...
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
updating tlmgr
updating existing packages
compilation failed- error
Unable to load picture or PDF file 'main_files/figure-pdf/cell-2-output-1.pdf'.
<to be read again>
}
l.203 ...ain_files/figure-pdf/cell-2-output-1.pdf}
```
Looking at `cell-2-output-1.pdf` I see that it is an empty 0kb file. If I force `--execute-daemon-restart` everything will then render fine.
I checked this against a notebook with just
```julia
using IJulia, CairoMakie
IJulia.register_mime(MIME("application/pdf"))
CairoMakie.activate!(type = "pdf")
lines(-2..2, sin)
```
and reevaluating the notebook file seems to generate the correct outputs. So, I don't think the issue is on the IJulia/CairoMakie side of things.
- Debian 11
- Quarto v1.3.34
- CairoMakie v0.9.3
- IJulia v1.23.3
### 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": "2022-12-05T22:33:35Z",
"creator": "agerlach",
"is_pull_request": false,
"labels": [
"bug",
"julia"
],
"locked": false,
"milestone": "v1.3",
"number": 3574,
"state": "closed",
"title": "CairoMakie Subsequent Renders Produce Empty Figure Files",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3574"
} |
### Bug description
Tables without a caption should not be numbered. In the following test document, the second table is captioned and is correctly numbered 1 with html output and incorrectly numbered 2 with pdf output. Rendered files are attached. Quarto version is 1.2.269. Linux version is Ubuntu 22.04.
````
---
title: test
format: pdf
##format: html
---
```{r, echo=FALSE, message=FALSE}
library(knitr )
opts_chunk$set(echo = FALSE
,message = FALSE)
library(gt)
library(tidyverse)
mt <- mtcars[1:4, 1:4]
```
```{r}
gt(mt) ## does not display a number
```
```{r}
#| label: tbl-num
#| tbl-cap: 'here is a caption using chunk options'
mt %>%
gt() ## table number is 1 in html and 2 in pdf
```
Here is a cross-reference to @tbl-num
```{r}
sessionInfo()
```
````
Rendered from command line; didn't use RStudio
[test_quarto.zip](https://github.com/quarto-dev/quarto-cli/files/10157208/test_quarto.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": "cscheid",
"comments": 2,
"created_at": "2022-12-05T19:19:26Z",
"creator": "rmcd1024",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3571,
"state": "closed",
"title": "Table numbering inconsistent between html and pdf (incorrect in pdf)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3571"
} |
I have the following common use case:
- writing a report with many qmd chapters
- each chapter calculates key facts (in R)
- up-front summary chapter reprises key facts in text with inline code and perhaps includes a summary table
Thus, I need to calculate the facts in the body-of-the-report chapters before executing the code for the summary chapter, but I want the summary to appear first. It would be great to define an execution order for the files and an appearance order for the files that may be different, so that I could calculate the summary chapter last but have it appear first.
There are workarounds, of course, such as:
- Calculate everything first - for example, R files executed at the start that do all calculations, and the qmd files merely report the results (tables, figures, inline text). But this makes for a potentially awkward and error-prone workflow as it requires thinking about the whole project and its presentation separately. A more-natural workflow (for me) is to develop the calculations at the same time and in the same place that I am figuring out how to present the information.
- Have every full execution create and save results into a prior-results folder. In the _next_ execution these results will be available to the summary chapter at the start. Requires being extra-careful that the results have not changed from one execution to the next, or putting in error checking to be sure that, after all files are executed, the current results are the same as prior results.
Neither of these seems as good as having the ability to separate execution order from appearance order.
Would love to hear if there are better workarounds - or perhaps quarto already has this capability and I haven't found it yet.
Many thanks.
| {
"assignee": null,
"comments": 2,
"created_at": "2022-12-05T11:36:48Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 3568,
"state": "open",
"title": "Feature request: For quarto book qmd files, allow execution order to differ from order appearing in book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3568"
} |
### Bug description
I'm starting to create a book, and it's rendered properly on a desktop monitor.
If I open it in a smartphone browser, the top title is not visible at all, and is covered by the section title.
Here a sample URL: https://aborruso.github.io/asud-vademecum-monitoraggi/cultura-dato/licenza.html
Here the source repo: https://github.com/aborruso/asud-vademecum-monitoraggi
I think it's a bug, because I do not have customized any style.
I'm using quarto 1.3.21 in debian 11.
Thank you
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [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": "2022-12-04T15:03:35Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3562,
"state": "closed",
"title": "HTML book rendering and titles margin top in mobile view",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3562"
} |
### Bug description
I expect this to fail because of unknown documentclass (or use the locally defined asdf), but it instead compiles with the default value for documentclass.
```
---
title: "Quarto Basics"
format:
pdf:
documentclass: asdf
---
# Hi
foo
```
If I remove one or both of the empty lines before the ending, `---` I get the expected behavior.
Gives the expected result: not compling
```
---
title: "Quarto Basics"
format:
pdf:
documentclass: asdf
---
# Hi
foo
```
same here
```
---
title: "Quarto Basics"
format:
pdf:
documentclass: asdf
---
# Hi
foo
```
I consider this to be a bug that should be fixed. Either not compile at all if empty lines before `---` exists or comile and parse YAML correctly.
# Environment
OS: Fedora 37
Editor: VScode.
quarto --version
```
1.2.269
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 6,
"created_at": "2022-12-03T23:28:41Z",
"creator": "crazyminecuber",
"is_pull_request": false,
"labels": [
"enhancement",
"upstream",
"lint"
],
"locked": false,
"milestone": "Future",
"number": 3560,
"state": "open",
"title": "yaml options are ignored if too many empty new lines are added",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3560"
} |
### Bug description
I want to [cross-reference to tables](https://quarto.org/docs/authoring/cross-references.html#tables) that are inside a tabset panel. It turns out that only if the table being referenced is _in the tab that is currently visible_, the cross-ref link would work. By contrast, if the cross-ref link refers to the table that is in the non-visible tab, then clicking the link doesn't do anything.
**`.qmd` file**
<pre>
---
title: "cross-refs to inside-tabset-panel-tables work only if those tables are already visible"
format: html
---
::: {.panel-tabset}
## iris
```{r}
#| label: tbl-iris
#| tbl-cap: Iris
knitr::kable(head(iris))
```
## mtcars
```{r}
#| label: tbl-mtcars
#| tbl-cap: Mtcars
knitr::kable(head(mtcars))
```
:::
---
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
## content; keep scrolling down
Here I want to refer to `mtcars` table from above: @tbl-mtcars
However, clicking on this cross-ref link would work only if _mtcars_ tab is already selected and visible up there.
Otherwise, if _iris_ tab is displayed above, then clicking on _mtcars_ cross-ref link here won't do anything.
</pre>
------
- Quarto version: `1.2.269`
- RStudio version: `2022.07.2+576 Spotted Wakerobin (desktop)`
<details>
<summary>Session Info</summary>
``` r
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.2.2 (2022-10-31 ucrt)
#> os Windows 8.1 x64 (build 9600)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz Asia/Jerusalem
#> date 2022-12-03
#> pandoc 2.19.2 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> - Packages -------------------------------------------------------------------
#> package * version date (UTC) lib source
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
#> digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.1)
#> evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.2)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.2)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.2)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.2)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
#> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
#> rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.2)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.2)
#> 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)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
#> xfun 0.34 2022-10-18 [1] CRAN (R 4.2.2)
#> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.1)
#>
#> [1] C:/Program Files/R/my_packages
#> [2] C:/Program Files/R/R-4.2.2/library
#>
#> ------------------------------------------------------------------------------
```
</details>
| {
"assignee": "cscheid",
"comments": 13,
"created_at": "2022-12-03T14:57:11Z",
"creator": "emmansh",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"crossref"
],
"locked": false,
"milestone": "v1.3",
"number": 3557,
"state": "closed",
"title": "Table cross-refs don't work when referring to tables in non-visible tabs (in tabset panel)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3557"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3151
<div type='discussions-op-text'>
<sup>Originally posted by **maxdrohde** November 2, 2022</sup>
In the `reveal.js` format, we can use the `output-location: column` YAML option to show the output in the column next to the code, instead of the standard location below the code (see: https://quarto.org/docs/presentations/revealjs/#output-location)
It seems to me like this is only possible in the `reveal.js` format. It would be great to have this supported in HTML documents as well.</div> | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-12-02T13:44:56Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3550,
"state": "open",
"title": "Support `output-location: column` in HTML documents",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3550"
} |
### Bug description
Hello quarto team,
I have an problem when I try to make a header from r code. My objective is to generate a header from a for loop and that this header is available from the table of contents. But, when I tried to use htmltools or knit_print.html I cannot make that the header appear in the TOC.
Please if anyone knows a way it will be awsome.
Thanks in advance,
Quarto code below:
```
---
title: "Untitled"
format: html
editor: visual
toc: true
toc-depth: 10
params:
a: ~disease + sex
---
## 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).
```{r}
params
```
```{r}
library(tidyverse)
library(plotly)
library(htmltools)
knit_print.html("<h2 class=`anchored` data-anchored-id=`HI`>HI</h2>")
htmltools::h3("HI")
plotlist<-list()
for (i in colnames(iris)) {
a<-as_tibble(iris) %>%
ggplot(aes(i,Sepal.Length))+
geom_point()
b<-as_tibble(iris) %>%
ggplot(aes(i,Sepal.Length))+
geom_line()
plotlist[[i]]<-list(h3("Hi"),ggplotly(a),ggplotly(b))
}
htmltools::tagList(plotlist)
for (i in 1:3) {
nam <- paste0("a_",i)
assign(nam,list(c(1,2,3)))
}
print(params$a)
```
### A
#### B
##### C
###### D
```
RStudio version:
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 4
minor 2.1
year 2022
month 06
day 23
svn rev 82513
language R
version.string R version 4.2.1 (2022-06-23)
nickname Funny-Looking Kid
Operating system:
Linux, Ubuntu 20.04 within a VMWare virtual machine.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-12-02T02:19:01Z",
"creator": "pipaber",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3548,
"state": "closed",
"title": "Header generated from htmltools don`t appear in the table of contents.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3548"
} |
### Bug description
I'm creating a website with images that update daily. However, users sometimes don't get the latest image because their browser shows them a cached copy. I found that adding `?1234` with a different number at each update can solve the issue.
So I created an R variable called date with the current date and then inserted the image like this:
```
```
The problem is that quarto now is not copying latest3.png to the correct docs directory. My guess is that it's looking for a latest3.png?20221201 file to copy it, but since it doesn't exist, it doesn't do it.
Reproducible example: https://github.com/eliocamp/asymsam-web/blob/4c9866320489526245c7ac5c47e804acade99e8a/monitoring/index.qmd
I'm running the latest version of quarto-cli on Debian GNU/Linux 9.13 (stretch).
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-12-01T17:13:19Z",
"creator": "eliocamp",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3543,
"state": "closed",
"title": "Images are not copied into docs if the link adds optional parameter (e.g. image.jpg?2134)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3543"
} |
### Bug description
It seems that Quarto doesn't apply the `fragment-index` to images:
```md
## How to Measure
::: {.incremental}
- Assume we have 2 variants of a website: `A` and `B`.
- How would we measure their design effect on user engagement?
:::
{.absolute bottom=0 .fragment .fade-in-then-out fragment-index=20}
```
The output will have `data-fragment-index=0` for the image.
In the case above I want the image to appear in sync with an item of the list.
So I'd like to be able to have `{.absolute bottom=0 .fragment .fade-in-then-out fragment-index=20}` yet what ever I do, I can't control its index.
Just as a note, it would be great to be able to have control on the index in `.incremental`. Maybe something like defining the index of the first item (Then all are chained)?
This is tested on Windows 10, VS Code, Quarto Extension `1.56` and Quarto CLI `1.2.269`.
### 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": "2022-12-01T08:03:18Z",
"creator": "RoyiAvital",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "Future",
"number": 3539,
"state": "open",
"title": "The `fragment-index` Has No Effect on Images for `Reveal.JS`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3539"
} |
### Bug description
For the quarto presentation (revealjs),
we will move to the first page if we click the hyperlinks of equation numbers.
It is OK for other hyperlinks, e.g. Theorem.
The following is an easy test `qmd` file.
```
---
title: "Untitled"
format: revealjs
---
## A
$$
\begin{aligned}
f(X) = y.
\end{aligned}
$$ {#eq-EEE}
## B
See @eq-EEE.
::: {#thm-TTT}
Lorem ipsum dolor sit amet, qui minim labore adipisicing minim sint cillum sint consectetur cupidatat.
:::
## C
See @thm-TTT.
```
My device:
- RStudio 2022.07.2 Build 576
- quarto version: 1.2.269
-
```
> sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
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": 3,
"created_at": "2022-12-01T05:41:46Z",
"creator": "ChoCho66",
"is_pull_request": false,
"labels": [
"bug",
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 3533,
"state": "closed",
"title": "Hyperlinks of equation numbers do not work in quarto presentation (revealjs)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3533"
} |
### Bug description
I have a custom format that includes some boilerplate stuff that I'd rather just pop into ancillary `.qmd` files and include in the template. I can use, for example, `{{< include _footer.qmd >}}` in my `template.qmd` and then add to my `_extension.yml`:
```yaml
contributes:
formats:
html:
format-resources:
- _footer.qmd
```
And `_footer.qmd` is correctly added to the extension subfolder when I `quarto use template`. However, the include resolves to the document folder, not the actual location the `_footer.qmd` was copied to in `_extensions/[extension name]/_footer.qmd`.
Although that might be expected considering where the include is copied to (the extension subfolder), other resources that are bundled, like extension stylesheets that are marked under the `css` key, are correctly resolved relative to the extension subfolder rather than the document.
Here's a repro extension:
```
_extensions/
ext-bundle-qmd/
_extension.yml
_footer.qmd
template.qmd
```
`template.qmd`:
````
---
title: Untitled
format:
ext-bundle-qmd-html: default
author: James Goldie
date: last-modified
---
## Introduction
*TODO* Create an example file that demonstrates the formatting and features of your format.
This format includes a nice little extra bit that is included in a separate file!
{{< include _footer.qmd >}}
````
`_extension.yml`:
```yaml
title: Ext-bundle-qmd
author: James Goldie
version: 1.0.0
quarto-required: ">=1.3.0"
contributes:
formats:
html:
theme: yeti
format-resources:
- _footer.qmd
```
`_footer.qmd`:
```
The footer includes some other nice things!
```
**Quarto version:** 1.3.21
**OS:** macOS 12.6.1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2022-12-01T04:01:37Z",
"creator": "jimjam-slam",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3531,
"state": "closed",
"title": "Relative paths for includes bundled with extensions are not resolved correctly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3531"
} |
### Bug description
If a package is loaded in a chunk where the execution option `echo` is set to `false` it seems that the `downlit` package does not find the corresponding function. It does not create a link.
````
---
format:
html:
code-link: true
---
```{r}
#| echo: false
library(ggplot2)
mtcars |>
ggplot(aes(x = mpg, y = disp)) +
geom_point()
```
`filter()`, `ggplot()`
````
---
RStudio version: 2022.07.2 Build 576
R version: 4.2.2
quarto version: 1.2.269
OS: macOS Ventura 13.0.1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-30T17:10:21Z",
"creator": "jwarz",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 3527,
"state": "open",
"title": "code-link does not work if echo: true is being used",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3527"
} |
### Bug description
`\r` and `\n` in math environments get interpreted as carriage return and line feed when using gfm
OS: OSX and Debian 11
Quarto v 1.3.34
````md
---
format: gfm
---
$$\left{a\right}$$
$$\nabla$$
````
renders as
````md
$$\left{a
ight}$$
$$
abla$$
````
### 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": "2022-11-30T17:04:01Z",
"creator": "agerlach",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 3526,
"state": "closed",
"title": "gfm improper handling of escapes in math environments",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3526"
} |
### Bug description
Hello,
I am trying to have a figure in a jupyter notebook (in python) with a figure caption that can be cross-referenced in the text.
Following the documentation [here](https://quarto.org/docs/authoring/figures.html), I put the follwing
```
::: {#fig-elephant}
Famous Elephants
:::
```
However, this leads to the following figure caption `FigureΒ 2: ?(caption)`. It does not work neither with the following code
```
::: {#fig-elephant}
:::
```
This bug is not present when one has two subfigures, as shown in the documentation.
```
::: {#fig-elephants layout-ncol=2}
{#fig-surus}
{#fig-hanno}
Famous Elephants
:::
```
Tested on Mac Os 12.0.1.
Thanks a lot for the 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": null,
"comments": 4,
"created_at": "2022-11-30T16:20:53Z",
"creator": "adauphin",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3525,
"state": "closed",
"title": "Figure caption missing for single figure",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3525"
} |
### Bug description
If `code-line-numbers: true` is used together with `code-link: true` only base-r functions outside of code blocks are being linked.
````
---
format:
html:
code-link: true
code-line-numbers: true # linking works with false
---
`filter()`, `ggplot()`
```{r}
library(ggplot2)
mtcars |>
ggplot(aes(x = mpg, y = disp)) +
geom_point()
```
````
---
Studio version: 2022.07.2 Build 576
R version: 4.2.2
quarto version: 1.2.269
OS: macOS Ventura 13.0.1
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cderv",
"comments": 0,
"created_at": "2022-11-30T12:38:16Z",
"creator": "jwarz",
"is_pull_request": false,
"labels": [
"bug",
"computations",
"source-code"
],
"locked": false,
"milestone": "v1.4",
"number": 3519,
"state": "open",
"title": "code-link and code-line-numbers do not work together",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3519"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3517
<div type='discussions-op-text'>
<sup>Originally posted by **jpatteet** November 30, 2022</sup>
I asked a question on stackoverflow and got an answer that resolved the problem. I am posting both here, maybe it is worth some modifications in quarto or not, let me know what you think.
**Question:**
I am wondering if it is possible to render quarto document faster.
When I render my document I get these messages in the "Background Jobs" window:
```
running xelatex - 1
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
running xelatex - 2
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
running xelatex - 3
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
```
All the way until:
```
running xelatex - 10
This is XeTeX, Version 3.141592653-2.6-0.999994 (TeX Live 2022) (preloaded format=xelatex)
restricted \write18 enabled.
entering extended mode
WARNING: maximum number of runs (9) reached
```
Output created:
Does anyone know what those 10 "running xelatex mean ? Is there a way to decrease this number of runs and what is the impact on the final rendering ?
**Answer:**
Quarto generates PDF via LaTeX by default. The LaTeX processors sometimes require multiple runs, as they step through the document sequentially and need a another run to, for example, update the table of contents after seeing another heading. Usually two runs are enough, but some LaTeX packages require more runs to get the correct output. Ten runs is quite unusual though, there might be something wrong elsewhere.
Quarto uses a heuristic to determine if it needs to run the LaTeX engine once more. Quarto also installs any missing LaTeX packages automatically. However, the tool latexmk is probably better in determining when to do additional calls to xelatex. You can use this tool with Quarto:
```
---
format:
pdf:
pdf-engine: latexmk
pdf-engine-opt: -xelatex
---
```
If the document still requires 10 runs, then there might be an issue with a LaTeX package somewhere.
**Comment:**
I added pdf-engine: latexmk and pdf-engine-opt: -xelatex and now it does not even tell me running xelatex and renders the document very quickly </div> | {
"assignee": "dragonstyle",
"comments": 10,
"created_at": "2022-11-30T10:31:28Z",
"creator": "jpatteet",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.4",
"number": 3518,
"state": "closed",
"title": "Quarto rendering pdf, running xelatex 10 times",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3518"
} |
If extensions are put in the wrong directory, quarto silently ignores them and it's hard to know which are there and which are not.
It would be nice if `quarto render` reported a list of all "enabled" extensions. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-11-29T21:13:08Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3510,
"state": "open",
"title": "quarto should report found extensions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3510"
} |
### Bug description
Hello,
I use R code to produce regression summary tables that include asterisks (`*`, `**`, or `***`). For html outputs, some asterisks disappear and some italics and bold section appear. It seems to be a confusion in quarto between markdow and html in this case.
Please find below a reproducible example. Github doesn't allow for *.qmd files, so I had to rename the extension to *.txt:
[reprex_bug_quarto_asterisk_qmd.txt](https://github.com/quarto-dev/quarto-cli/files/10116808/reprex_bug_quarto_asterisk_qmd.txt)
My RStudio version is `2022.07.2 Build 576` (Spotted Wakerobin)
It is running on Windows 11 (I get the same issue on Ubuntu).
### 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": "2022-11-29T19:57:09Z",
"creator": "fBedecarrats",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3509,
"state": "closed",
"title": "Asterisk in html output tables in get converted to markdown (ie. italics and bold marks)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3509"
} |
### Bug description
# Syntax highlighting and line numbering break in code blocks for the VHDL language
Observed in `quarto 1.2.269` running on `Windows 11 pro version 10.0.22621`.
Description: VHDL code which includes `process` statements breaks syntax highlighting and further processing like line-numbering. It appears to be a parsing issue at `end process;`. If you write instead the (syntactically incorrect) `end;` or `end process;process;` then the code block is rendered correctly.
When this issue happens, quarto's output includes the following warning
```
[WARNING] Could not highlight code block:
Capture 1 not defined!
```
Minimal self-contained example:
````qmd
---
title: Example
subtitle: VHDL syntax highlighting doesn't work
format: beamer
---
## Invalid VHDL, renders ok
```{.vhdl code-line-numbers="true"}
architecture arch of dff is
begin
ff: process (clk)
begin
if clk'event and clk='1' then
q <= d;
end if;
end process;process;
end arch;
```
## Valid VHDL, syntax highlighting and line numbering don't work
```{.vhdl code-line-numbers="true"}
architecture arch of dff is
begin
ff: process (clk)
begin
if clk'event and clk='1' then
q <= d;
end if;
end process;
end arch;
```
````
### 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": "2022-11-29T17:54:47Z",
"creator": "fmirandabonomi",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3506,
"state": "closed",
"title": "Syntax highlighting fails for correct VHDL code.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3506"
} |
### Bug description
The header:
````md
---
author:
- name: 'peacecop kalmer:'
title: "MMS inimese organismis ja ΓΌmbritsevas keskkonnas"
output-file: ../../_book/keemia-mms.html
format:
revealjs:
incremental: true
self-contained: true
---
````
The content:
````md
## $`r if (knitr::is_html_output()) { "\\require{mhchem}" }`\ce{NaClO_2}$ vesilahuse tegemine tekstiliselt
````
Look into TOC and see the following:
````
\(\require{mhchem}\ce{NaClO_2}\) vesilahuse tegemine tekstiliselt
````
### 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": "2022-11-29T16:58:55Z",
"creator": "piiskop",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3503,
"state": "closed",
"title": "TOC shows unrendered R and LaTeX code",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3503"
} |
### Bug description
I'm on Windows 10 and Quarto can't seem to detect my Python installation.
```
Nom de lβhΓ΄te: L108235
Nom du systΓ¨me dβexploitation: Microsoft Windows 10 Entreprise
Version du système: 10.0.19044 N/A build 19044
Fabricant du systΓ¨me dβexploitation: Microsoft Corporation
```
```
C:\Users\mdesautels>py --list
-V:3.11 * Python 3.11 (64-bit)
-V:3.9
-V:ContinuumAnalytics/Anaconda39-64 Anaconda py39_4.12.0
C:\Users\mdesautels>quarto check
[>] Checking Quarto installation......OK
Version: 1.2.269
Path: C:\Users\mdesautels\AppData\Local\Programs\Quarto\bin
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[>] Checking R installation...........OK
Version: 4.2.1
Path: C:/ProgrammesMAD/R-4.2.1
LibPaths:
- C:/ProgrammesMAD/R-4.2.1/library
rmarkdown: 2.18
[>] 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": "cderv",
"comments": 10,
"created_at": "2022-11-29T15:32:38Z",
"creator": "desautm",
"is_pull_request": false,
"labels": [
"windows"
],
"locked": false,
"milestone": null,
"number": 3500,
"state": "closed",
"title": "Python installation not detected by Quarto when using pyenv-win install on Windows",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3500"
} |
### Bug description
Minor issues with the `fig-scap:` when there are multiple subfigures. When using subfigures and subcaptions, the `fig-scap` is no longer used in the list of figures, instead the full caption is used and the `scap` is ignored.
````md
---
title: "scratch"
toc: true
format:
pdf:
table-of-contents: true
lof: true
---
```{r}
#| fig-cap: "Long caption 1."
#| fig-scap: "Short1"
#| echo: false
plot(mtcars)
```
```{r}
#| layout-ncol: 2
#| label: fig-charts
#| echo: false
#| fig-cap: "Overall longer caption."
#| fig-scap: "Short2"
#| fig-subcap:
#| - "Long caption 2."
#| - "Long caption 3."
plot(mtcars)
plot(cars)
```
````
Related to this as well is the potential for using `scap` in divs for markdown figures, `![]()`. Not necessarily a bug as I'm unsure if scap is supported for HTML output.
RStudio Build 576. MacOS 12.6, Intel Macbook Pro 15-inch (2017).
### 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": "2022-11-29T08:59:49Z",
"creator": "BradyAJohnston",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3498,
"state": "open",
"title": "Support `-scap` in Float crossrefs consistently across formats and input options",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3498"
} |
### Bug description
I don't know whether it's a bug or expected behavior, given [@cscheid's comment](https://github.com/quarto-dev/quarto-cli/discussions/3253#discussioncomment-4128818) about rendering tables in Quarto being a work-in-progress. Anyhow, it's currently a limitation of Quarto.
`.qmd` file:
<pre>
---
title: "Table output of SQL code exceeds right border when code chunk is inside a tabset panel"
---
```{r}
library(DBI)
library(duckdb)
library(nycflights13)
```
```{r}
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = ":memory:")
dbWriteTable(con, "flights", nycflights13::flights, overwrite = TRUE)
```
::: {.panel-tabset}
## SQL
```{sql, connection=con}
SELECT *
FROM flights;
```
:::
</pre>
## rendered output
I had to zoom out my browser to level of 33% to capture it all
Instead, I would expect the table to be inside the tab's boundaries, with a horizontal scroll bar.
-------
- Quarto version: `1.2.269`
- RStudio version: `2022.07.2+576 Spotted Wakerobin (desktop)`
<details>
<summary>Session Info</summary>
``` r
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.2.2 (2022-10-31 ucrt)
#> os Windows 8.1 x64 (build 9600)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz Asia/Jerusalem
#> date 2022-11-29
#> pandoc 2.19.2 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> - Packages -------------------------------------------------------------------
#> package * version date (UTC) lib source
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
#> digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.1)
#> evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.2)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.2)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.2)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.2)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
#> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
#> rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.2)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.2)
#> 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)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
#> xfun 0.34 2022-10-18 [1] CRAN (R 4.2.2)
#> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.1)
#>
#> [1] C:/Program Files/R/my_packages
#> [2] C:/Program Files/R/R-4.2.2/library
#>
#> ------------------------------------------------------------------------------
```
<sup>Created on 2022-11-29 with [reprex v2.0.2](https://reprex.tidyverse.org)</sup>
</details>
| {
"assignee": null,
"comments": 0,
"created_at": "2022-11-29T08:17:45Z",
"creator": "emmansh",
"is_pull_request": false,
"labels": [
"enhancement",
"tables"
],
"locked": false,
"milestone": "v1.3",
"number": 3497,
"state": "closed",
"title": "Table output of SQL code exceeds right border when code chunk is inside a tabset panel",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3497"
} |
### Bug description
With the recent addition of the `rel: me` option to navbars, it's now possible to include a link to a Mastodon profile and have it be verified on their end:
```yaml
website:
title: "Blah"
navbar:
right:
- icon: mastodon
aria-label: mastodon
href: https://fediscience.org/@andrew
rel: me
```
Mastodon profile links typically include a `@` in their URL, like `https://fediscience.org/@andrew` above. This causes a minor problem when working with citations, just like Twitter card issues in https://github.com/quarto-dev/quarto-cli/issues/1702. When a site's navbar has a URL with a `@`, it causes a pandoc warning:
```
[WARNING] Citeproc: citation andrew not found
```
It's not a breaking bug or anything, just kind of funny to see it happen with every page that gets rendered π
---
This is with Quarto 1.3.26 in RStudio 2022.07.2+576 (and also in VS Code) on macOS Monterey 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": 5,
"created_at": "2022-11-28T22:40:03Z",
"creator": "andrewheiss",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3493,
"state": "open",
"title": "Citeproc warning when using a Mastodon profile link",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3493"
} |
### Bug description
The `output-dir` yaml parameter is only being pulled from the top-level `_quarto.yml` file. My expectation was that I could set a sub-directory specific, or file specific `output-dir` parameter.
I created a [simple repository to demonstrate the issue](https://github.com/anielsen001/quarto_output_dir_issue) since it requires more than 1 file to demonstrate. (The README.md in the repo contains similar information as this report.)
To demonstrate the issue run:
```bash
quarto render sub1/sub1.qmd
```
The file `sub1/sub1.qmd` contains the yaml:
```yaml
---
title: sub topic 1
output-dir: ../docs
---
```
The expected result is the output in the `docs` directory but the output is created in the `sub1` directory.
Running quarto yields the following terminal output
```
quarto render sub1/sub1.qmd
pandoc
to: html
output-file: sub1.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
output-dir: ../docs
title: sub topic 1
Output created: sub1.html
```
Adding the `output-dir` parameter to `sub1/_metadata.yml` does not change the result.
I'm using:
- quarto version 1.1.141
- Ubuntu Linux 20.04, 5.15.0-53-generic # 59~20.04.1-Ubuntu SMP Thu Oct 20 15:10:22 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
- VSCode as IDE, but running quarto from terminal CLI
### 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": "2022-11-28T13:16:34Z",
"creator": "anielsen001",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3487,
"state": "closed",
"title": "`output-dir` parameter only used in top-level `_quarto.yml` file",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3487"
} |
### Bug description
I'm on Apple M1, downloaded the dmg file for mac and installed Quarto. Everything completed successfully. Quarto files are under Macintosh HD/Applications/quatro. Opened the terminal and typed `quarto --help` and i'm getting
`zsh: command not found: quarto`
Yes, I'm using zshell.
Ideas?
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-11-28T10:46:53Z",
"creator": "edoson",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "v1.3",
"number": 3484,
"state": "closed",
"title": "[Mac M1] - quarto not recognized in terminal after installation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3484"
} |
### Bug description
Quarto fails to render author name attributes when rendering as `pdf`.
```
---
title: test
format: pdf
author:
- name:
given: John
family: Smith
literal: John Smith
---
```
The `yaml` above returns `true` instead of `John Smith`.
Using the following works:
```
---
title: test
format: pdf
author:
- name: John Smith
---
```
Tested in RStudio `2022.7.2.576`, Quarto `1.2.269` on MacOS `12.3.1`.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-28T09:36:08Z",
"creator": "arnaudgallou",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3483,
"state": "closed",
"title": "Author name attributes return `true` when rendering as `pdf`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3483"
} |
It seems like there are some issues in locating deno in `configure.cmd` script.
Tested on Windows 11 Education (Version 10.0.22621 Build 22621).
## Output
``` bash
configure.cmd
find: '/I': No such file or directory
find: 'deno.exe': No such file or directory
"Translated/recorded configuration settings from unix configuration script"
Bootstrapping Deno...
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
37 26.8M 37 10.1M 0 0 9953k 0 0:00:02 0:00:01 0:00:01 9953k
100 26.8M 100 26.8M 0 0 16.1M 0 0:00:01 0:00:01 --:--:-- 27.2M
tar: This does not look like a tar archive
tar: Skipping to next header
tar: Exiting with failure status due to previous errors
.
Configuring Quarto from C:\test\quarto-cli\package\src
'"C:\test\quarto-cli\\package\dist\bin\tools\deno.exe"' is not recognized as an internal or external command,
operable program or batch file.
Configuration done
Revendoring quarto dependencies
Downloading Deno Stdlib
'C:\test\quarto-cli\\package\dist\bin\tools\deno.exe' is not recognized as an internal or external command,
operable program or batch file.
NOTE: To use quarto please use quarto-cmd (located in this folder) or add the following path to your PATH
C:\test\quarto-cli\\package\dist\bin
``` | {
"assignee": "cderv",
"comments": 5,
"created_at": "2022-11-27T17:12:19Z",
"creator": "jooyoungseo",
"is_pull_request": false,
"labels": [
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 3477,
"state": "closed",
"title": "cannot locate deno: issue with configure.cmd",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3477"
} |
In [CONTRIBUTING.md#L21](https://github.com/quarto-dev/quarto-cli/blob/main/CONTRIBUTING.md?plain=1#L21), it says:
> # configure for your platform (./configure-macos.sh, ./configure-linux.sh, or ./configure-windows.cmd
However, there are only two configure files without platform name: "configure.cmd" and "configure.sh"
This needs clarification. | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-27T16:56:57Z",
"creator": "jooyoungseo",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3476,
"state": "closed",
"title": "Need to clarify configure file per OS platform",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3476"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3336
<div type='discussions-op-text'>
<sup>Originally posted by **AlFontal** November 15, 2022</sup>
As far as I know, it's possible to select a single location to show the Table of Contents, but while the dynamic TOC that always stays on the right is useful, sometimes I also want to show a full TOC just after the header in an article/blog post.
Is there any mechanism to have it behave like that right now?</div> | {
"assignee": "allenmanning",
"comments": 4,
"created_at": "2022-11-27T15:30:19Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"enhancement",
"websites"
],
"locked": false,
"milestone": "v1.4",
"number": 3473,
"state": "closed",
"title": "Ability to show the TOC both in body and right simulataneously",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3473"
} |
### Bug description
Following the ["Metadata Listings" section](https://quarto.org/docs/websites/website-listings-custom.html#metadata-listings) in the documentation, it is possible to include custom metadata in YAML, either in individual files or in front matter, and have that metadata show up in a custom listing template.
For instance, we can create a listing page:
**index.qmd**
````
---
title: "Testing"
template: custom.ejs
contents:
- name: First Item
href: https://www.quarto.org
custom-field: A **custom value**
- name: Second Item
href: https://www.rstudio.org
custom-field: A *second* custom value
---
Blah
````
β¦and a custom EJS template:
**custom.ejs**
````
```{=html}
<ul>
<% for (const item of items) { %>
<li>
<a href="<%- item.href %>"><%= item.name %></a><br/>
<%= item['custom-field'] %>
</li>
<% } %>
</ul>
```
````
β¦and it will render the custom field in an HTML list:
```
<ul>
<li>
<a href="https://www.quarto.org/">
First Item
</a><br>
A **custom value**
</li>
<li>
<a href="https://www.rstudio.org/">
Second Item
</a><br>
A *second* custom value
</li>
</ul>
```
However, any Markdown formatting in the custom field is *not* renderedβit renders the text as `A **custom value**` instead of `A <strong>custom value</strong>`
It could be helpful to have a helper function of sorts accessible by EJS files, like
```
<%= parseMarkdown(item['custom-field']) %>
```
Rendering works as expected when raw HTML is used in the metadata. That is,
```
- name: First Item
href: https://www.quarto.org
custom-field: A <strong>custom value</strong>
```
β¦ turns into
```
<li>
<a href="https://www.quarto.org/">
First Item
</a><br>
A <strong>custom value</strong>
</li>
```
---
This is with Quarto 1.3.26 in RStudio 2022.07.2+576 (and also in VS Code) on macOS Monterey 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": 1,
"created_at": "2022-11-27T04:32:10Z",
"creator": "andrewheiss",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3468,
"state": "open",
"title": "Markdown in custom listing fields not rendered by EJS template",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3468"
} |
### Bug description
When trying to render a quarto notebook with Python code from the command line I'm seeing behavior consistent with a persistent jupyter kernel. I would expect that each call to `quarto render` would run in a new, clean kernel.
For example consider the file `test.qmd` with the text
````
---
title: "Test"
author: "Test"
jupyter: python3
---
Test test test.
```{python}
import multiprocessing
multiprocessing.set_start_method("fork")
```
````
If I run
```
quarto render test.qmd --to html
```
from the command line once then everything renders fine, but I do see some `Python` threads that persist even after the command line prompt has returned.
If I run the same command again then quarto fails with the error
````
Executing 'test.ipynb'
Cell 1/1...ERROR:
An error occurred while executing the following cell:
------------------
import multiprocessing
multiprocessing.set_start_method("fork")
------------------
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
Input In [3], in <cell line: 2>()
1 import multiprocessing
----> 2 multiprocessing.set_start_method("fork")
File /usr/local/Cellar/[email protected]/3.9.6/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/context.py:243, in DefaultContext.set_start_method(self, method, force)
241 def set_start_method(self, method, force=False):
242 if self._actual_context is not None and not force:
--> 243 raise RuntimeError('context has already been set')
244 if method is None and force:
245 self._actual_context = None
RuntimeError: context has already been set
RuntimeError: context has already been set
````
Force quitting those dangling Python threads does allow me to render again without problem.
If I include a cell like
````
```{python}
print(locals())
a = 2
print(locals())
```
````
then I also see the `locals()` dictionary growing from call to call, even holding variables from previous renders that are no longer in the notebook, consistent with the kernel persisting from call to call.
Operating System: MacOS 10.15.7 (19H2026)
Python Version: Python 3.9.6 (default, Jun 29 2021, 06:20:32) [Clang 12.0.0 (clang-1200.0.32.29)] on darwin
Quarto Version: 1.1.251
Any help would be appreciated, and apologies if I'm missing something obvious. Many thanks for a great project.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 10,
"created_at": "2022-11-26T22:17:18Z",
"creator": "betanalpha",
"is_pull_request": false,
"labels": [
"bug",
"verify-fixed"
],
"locked": false,
"milestone": "v1.4",
"number": 3466,
"state": "open",
"title": "quarto command line function failing to close jupyter kernel?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3466"
} |
### Bug description
Hello,
I can not use/create bash aliases in quarto bash chunks.
The following returns nothing [it should show the list of available aliases]
````
```{bash}
alias
```
````
Assigning new aliases returns this error: "`/usr/bin/bash: line 2: l: command not found`"
````
```{bash}
alias l='ls -CF'
l
```
````
The same commands work fine in the terminal windows.
****
Another related question:
Is it possible to allow commands in a single chunk effective outside of the chunk. I mean, if I changed the working directory in a specific chunk, this is only effective inside of this chunk; i.e., the working directory in the next chunk returns to the home directory.
This same issue also implements to variables:
````
```{bash}
x=10
echo $x # this prints 10
```
````
````
```{bash}
echo $x # Nothing printed!
```
````
****
Thanks, Ahmed
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-26T21:50:55Z",
"creator": "elgabbas",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3465,
"state": "closed",
"title": "bash aliases not recognized in quarto",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3465"
} |
### Bug description
In https://github.com/quarto-dev/quarto-cli/commit/0f56fc0aabe39778f5aab79c5ad4bef27307776c, the `subtitle` field was added as an option for sidebars. It also pops up as a valid option in RStudio:
<img width="549" alt="image" src="https://user-images.githubusercontent.com/73663/204073770-15bcd9ad-2be9-4e7d-81f2-d7e9aea4ecf5.png">
However, with Quarto 1.2.269, the subtitle does not get generated when using this YAML:
**_quarto.yml**
```yaml
project:
type: website
website:
title: "Site title"
sidebar:
title: "Sidebar title"
subtitle: "Here's a subtitle for the sidebar"
contents:
- text: "About"
- text: "Blog"
```
It renders like thisβthe sidebar-specific title overrides the site title, as expected, but no subtitle appears:
<img width="265" alt="image" src="https://user-images.githubusercontent.com/73663/204073855-eb7a3b36-02de-4f8b-b077-f10df83c1424.png">
It doesn't look like a theme issueβthe HTML for the subtitle just doesn't get generated:
```html
<div class="pt-lg-2 mt-2 text-left sidebar-header">
<div class="sidebar-title mb-0 py-0">
<a href="http://localhost:3580/">Sidebar title</a>
</div>
</div>
<div class="mt-2 flex-shrink-0 align-items-center">
<div class="sidebar-search">...</div>
</div>
<div class="sidebar-menu-container">
<ul class="list-unstyled mt-1">
<li class="sidebar-item">About</li>
<li class="sidebar-item">Blog</li>
</ul>
</div>
```
---
This is with Quarto v1.2.269 in RStudio 2022.07.2+576 (and also in VS Code) on macOS Monterey 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": null,
"comments": 1,
"created_at": "2022-11-26T05:45:10Z",
"creator": "andrewheiss",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3462,
"state": "closed",
"title": "Sidebar subtitle not rendering",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3462"
} |
### Bug description
I have a qmd file as follows named `hard-line-breaks.qmd`:
```markdown
---
title: "Hard Line Breaks"
format:
html:
md_extensions: +hard_line_breaks
---
these
words
should
be
on
seperate
lines
```
If I run `pandoc -f markdown+hard_line_breaks -t html hard-line-breaks.qmd` I get the following. Note how `+hard_line_breaks` includes a `<br>` after every word. So far so good.
```html
<p>these<br />
words<br />
should<br />
be<br />
on<br />
seperate<br />
lines</p>
```
However, if I run `quarto render hard-line-breaks.qmd`, I get the following output (top and bottom truncated for brevity):
```html
<p>these words should be on seperate lines</p>
```
Am I doing something wrong? How can I successfully activate the extension [`hard_line_breaks`](https://pandoc.org/MANUAL.html#extension-hard_line_breaks)?
```
> quarto --version
1.2.269
> lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 22.04.1 LTS
Release: 22.04
Codename: 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": null,
"comments": 3,
"created_at": "2022-11-26T00:33:20Z",
"creator": "ratnanil",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3461,
"state": "closed",
"title": "Quarto does not respect my markdown extension",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3461"
} |
### Bug description
Hello,
I am rendering a website on Windows 10 with the Quarto extension v1.56.0 on VS Code v1.73.1. I have tried and failed to change the active link color in the Table of Contents using CSS. I know that I am specifying the right CSS class because the style sheet below will affect the link boldness and background color, but not the link color itself. I have tried this with and without `!important`.
```
.toc-active .nav-link.active {
color: red !important;
background-color: yellow;
font-weight: bold;
}
```
The link text remains blue (example below).
Here's a reproducible yaml and index.qmd:
YAML:
```
project:
type: website
website:
title: "example"
navbar:
left:
- href: index.qmd
text: Home
- about.qmd
format:
html:
theme: cosmo
css: styles.css
toc: true
```
index.qmd:
```
---
title: "example"
---
This is a Quarto website.
## Section 1
To learn more about Quarto websites visit <https://quarto.org/docs/websites>.
## Section 2
Example
## Section 3
Example
## Section 4
Example
### Subsection 1
Example
## Section 5
Example
```
Any advice appreciated!
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-25T21:30:07Z",
"creator": "lawalter",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3460,
"state": "closed",
"title": "Can't specify TOC link color with CSS",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3460"
} |
### Bug description
Still looking for a good solution to https://github.com/quarto-dev/quarto-cli/issues/135, I found https://github.com/minrk/allthekernels which seems like a great candidate: it's a simple Jupyter kernel that forwards code cells to different sub-kernels for different languages (this also seems to be the approach favored by the Jupyter developers, see https://github.com/jupyterlab/jupyterlab/issues/2815).
However I found some issues trying to use it with Quarto. Here's my test document `a.qmd`:
---
jupyter: atk
---
```{any}
>python3
import matplotlib.pyplot as plt
plt.plot([1, 2, 3, 4])
2+2
```
```{any}
>octave
plot(magic(2))
2+2
```
First, two issues that should be fixed outside of Quarto I think:
* Calling `quarto render a.qmd` gives `ERROR: TypeError: Cannot read properties of undefined (reading 'toLowerCase')`. This is because the `kernel.json` doesn't define a language. The language key is [required](https://jupyter-client.readthedocs.io/en/stable/kernels.html#kernel-specs) so this should probably be fixed in allthekernels. I fixed it by adding `"language": "any"` in the `kernel.json`.
* With the above fix, calling `quarto render a.qmd` sometimes produces an HTML file with code cells but empty outputs. It looks like a latency issue: it normally works the second time (once the daemon is running). The same issue can be observed when running the cells in Jupyter Notebook so it's probably a problem in allthekernels.
Now the issue that should be fixed in Quarto I think: The execution requires that I mark code blocks with `{any}` to match the language declared in `kernel.json`. Due to this the code blocks are not formatted properly: no syntax highlighting and not even a gray background. What I would expect instead is to write
```{octave}
>octave
plot(magic(2))
2+2
```
and have it work as long as I have defined `jupyter: atk`. If this worked I could also write a Lua filter to infer the `>octave` line from the block language and insert it automatically.
Note: the same issue affects the [SoS](https://vatlab.github.io/sos-docs/) kernel (another polyglot kernel that additionally enables data exchange between the sub-kernels).
Tested with quarto 1.2.269 and 1.3.26 on Pop!_OS 22.04.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-25T17:37:41Z",
"creator": "knuesel",
"is_pull_request": false,
"labels": [
"enhancement",
"jupyter"
],
"locked": false,
"milestone": "Future",
"number": 3459,
"state": "open",
"title": "Code block language not working with \"allthekernels\" kernel",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3459"
} |
### Bug description
This anomaly occurs in RStudio Server. i had created a QMD-file inside a subfolder that was inside a subfolder. Testing via Render was no problem. Suddenly rendering did not work anymore and instead of a rendered presentation a rendered webpage was displayed in Presentation view.
i created a test file and that was rendered fine. i even copied and pasted the content of the test file into the first-mentioned file and rendering did not work. In Jobs:
Watching files for changes
/presentation_files/libs/revealjs/dist/reset.css (404: Not Found)
/presentation_files/libs/revealjs/dist/reveal.css (404: Not Found)
/presentation_files/libs/revealjs/plugin/quarto-line-highlight/line-highlight.css (404: Not Found)
These files are all there, i mean in the subfolder of the subfolder.
Renaming the file made rendering work correctly however Presentation view would not show any changes inside the file afterward.
> RStudio Server
> 2022.02.2 Build 485
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description: Ubuntu 20.04.5 LTS
> Release: 20.04
> Codename: focal
### 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": 2,
"created_at": "2022-11-25T17:01:39Z",
"creator": "piiskop",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": "Future",
"number": 3458,
"state": "closed",
"title": "Presentation view does not update automatically.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3458"
} |
### Bug description
Hi,
I have really strange table rendering problems.
My code is the one below. If I render it, the python ouput table is printed as plain text
If I change `{r}` in `{{r}}`, and render again the file, I have the correct rendering of the python ouput table
It seems to me that something does not work properly, but it seems to me that the code has no errors.
I'm using quarto 1.3.21, in debian 11 (inside WSL2).
Thank you
~~~~
---
title: "tables test"
format: html
---
```{python}
import pandas as pd
df = pd.read_csv("input.csv")
df
```
```{r}
library(tidyverse)
data <- read_csv('input.csv')
knitr::kable(data)
```
~~~~
```
year,i,v
2016,F,0.9599716561118586
2016,G,0.0382418519682473
2016,C,0.0012657864805693667
2016,W,1.2161279236855405e-05
2016,S,4.5402109150926846e-05
```
### 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": "rich-iannone",
"comments": 5,
"created_at": "2022-11-25T15:41:39Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [
"enhancement",
"upstream",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 3457,
"state": "open",
"title": "coexistence of R and Python gives me inconsistent table renderings",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3457"
} |
In `quarto preview --help` output, the following line needs a space:
> Automatically reloads the browser *wheninput* files or document resources
* "wheninput" -> "when input"
Tested in quarto version 1.3.26:
| {
"assignee": "jooyoungseo",
"comments": 3,
"created_at": "2022-11-25T02:08:10Z",
"creator": "jooyoungseo",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3452,
"state": "closed",
"title": "Missing space in quarto preview --help output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3452"
} |
### Bug description
Hi - I'm getting the error below when attempting to push my [Quarto](https://www.quantumjitter.com/) site to Github for continuous deployment using the [Github Action](https://quarto.org/docs/publishing/netlify.html#github-action) approach. `publish.yml` is set up per [this doc](https://quarto.org/docs/publishing/netlify.html#publish-action).
> To https://github.com/cgoo4/quantumjitter.git
> ! [remote rejected] HEAD -> main (refusing to allow a Personal Access Token to create or update workflow `.github/workflows/publish.yml` without `workflow` scope)
> error: failed to push some refs to 'https://github.com/cgoo4/quantumjitter.git'
I've instead used the [publish-from-git-provider](https://quarto.org/docs/publishing/netlify.html#publish-from-git-provider) approach which is working fine.
RStudio: Version 2022.12.0-daily+295 (2022.12.0-daily+295)
macOS Monterey version 12.6
### 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": 2,
"created_at": "2022-11-24T17:26:37Z",
"creator": "cgoo4",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3450,
"state": "closed",
"title": "Unable to Push to Github for continuous deployment to Netlify",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3450"
} |
Building on this previous question about pdf in quarto books #1270, can you insert a pdf into a quarto document - for example as you can in latex? https://stackoverflow.com/questions/2739159/inserting-a-pdf-file-in-latex
_Originally posted by @PublicHealthDataGeek in https://github.com/quarto-dev/quarto-cli/issues/1270#issuecomment-1326643660_
Many thanks
| {
"assignee": null,
"comments": 1,
"created_at": "2022-11-24T16:39:49Z",
"creator": "PublicHealthDataGeek",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3447,
"state": "closed",
"title": "Can you insert a pdf into a quarto document?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3447"
} |
### Bug description
When using OJS code cells in a Quarto file, I do not get any output in the rendered HTML.
Hyperlink to .qmd file in GitHub repo: https://github.com/larnsce/ojs-test-drive/blob/main/ojs-test-drive.qmd
I tried to add the .qmd file here, but GiHub does not allow me to upload it.
# My rendered document
A screenshot of my HTML output file below.
# Session Info
- RStudio Version: 2022.7.2.576
- R version 4.2.1 (2022-06-23)
- Platform: x86_64-apple-darwin17.0 (64-bit)
- Running under: macOS Monterey 12.5.1
### Checklist
- [ ] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] 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": 5,
"created_at": "2022-11-24T15:21:19Z",
"creator": "larnsce",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3446,
"state": "closed",
"title": "No ouput from OJS code cells in rendered HTML",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3446"
} |
I think we're forwarding self-contained: true to pandoc's embed-resources: true but we're not passing embed-resources directly. This is a bug, right?
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3436
<div type='discussions-op-text'>
<sup>Originally posted by **dmacoritto** November 23, 2022</sup>
Hello everyone,
I am trying to switch from RMarkdown to Quarto and I have run into a challenge with the embed-resources YAML option. I would like to output an HTML document which is a standalone document with no dependencies.
Below is a screenshot of the YAML options for my document.
My issue is that, despite having included the "embed-resources: true" in the YAML, I get an external *_files folder that includes the required libraries to run the document (see below). My charts are indeed embedded in my HTML document but not my libraries. Is there a way to get a complete self-contained document with no dependencies to a *_files folder ?
Thank you very much for your help.
Darko</div> | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-11-24T14:38:00Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3445,
"state": "open",
"title": "embed-resources returns a libs folder",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3445"
} |
### Bug description
IDE: VScode with Quarto 1.2.269
OS: Windows 11
Description:
Suppose I create a default web project.
Then I open the code wrap and line number in configs as below:
````yml
format:
html:
code-line-numbers: true
code-overflow: wrap
````
Then if I have a code block with a very long line, it will look bad, as shown below in the first code block:
I have to close the code line number to make the wrapping code overflow works, as the second code block. The problem exists in different themes and fonts too.
### 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": "2022-11-24T06:23:20Z",
"creator": "WAcry",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 3442,
"state": "open",
"title": "code wrap incorrectly with line number",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3442"
} |
### Bug description
I've noticed that the styling of cross-references (e.g., to chapters) differs for HTML and PDF output.
I'm using R Studio with R version 4.2.2. Running Quarto 1.2.258 on a Windows computer.
**Minimal Reproducible Example:**
```
---
title: "HTML / PDF Cross-Rerefence Test"
# CROSS-REFERENCING
number-sections: true
# STYLING
format:
html:
theme: cosmo
pdf:
documentclass: scrreprt
toc-title: "Inhoud"
toc-depth: 2
link-citations: true
---
# This would be Chapter 1 {#sec-chap-1}
# This would be Chapter 2
With a link to @sec-chap-1
```
**Output: HTML**
**Output: PDF**
**Expected Behavior:**
I would expect the PDF link to include the 'Section' - which is what is what is currently happening in the HTML styling. Underlining the link would also be nice for clearer visibility, but not necessary (could perhaps be achieved through custom css). At the moment with only the numbers as links it is very hard for readers to recognize that there is in fact a link!
### 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": "2022-11-23T14:18:44Z",
"creator": "SHogenboom",
"is_pull_request": false,
"labels": [
"duplicate",
"enhancement",
"crossref"
],
"locked": false,
"milestone": "Future",
"number": 3440,
"state": "closed",
"title": "FR: Uniform Cross-Reference Styling",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3440"
} |
### Bug description
Consider the following minimal working example:
``````
---
title: "MWE"
format: docx
---
## Quarto
Quarto enables you to weave together content and executable code into a finished document.
To learn more about Quarto see <https://quarto.org>.
::: {#fig-r-logos layout-ncol="2"}
{#fig-r-logo-1}
{#fig-r-logo-2}
Awesome Programming Language Logo.
:::
``````
`quarto render mwe.qmd` produces
Note the subfigures overflow the width available.
# Expected Output
Subfigure is resized to fit in the available space.
# Supporting Files
[mwe.zip](https://github.com/quarto-dev/quarto-cli/files/10074059/mwe.zip)
# Environment Information
```
[β] Checking Quarto installation......OK
Version: 1.2.79
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 7,
"created_at": "2022-11-23T09:22:00Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"enhancement",
"docx"
],
"locked": false,
"milestone": "v1.4",
"number": 3435,
"state": "open",
"title": "Subfigure overflows width available space. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3435"
} |
### Bug description
Word format doesn't respect PART and its contents in Quarto Book, they will be auto removed.
<img width="1103" alt="ζͺε±2022-11-23 11 41 18" src="https://user-images.githubusercontent.com/12031874/203467265-7075d424-198a-4ef8-8d50-38d361593d19.png">
## reproduce
<https://github.com/XiangyunHuang/quarto-broken> is a minimal Quarto book project which created from Quarto Book skeleton. Only one more file `getting-started.qmd` was added, its content as follow:
```
# getting started
hello
```
This is `_quarto.yml`
```
project:
type: book
book:
title: "quarto-test"
author: "Jane Doe"
date: "11/23/2022"
chapters:
- index.qmd
- part: getting-started.qmd
chapters:
- intro.qmd
- summary.qmd
- references.qmd
bibliography: references.bib
format:
html:
theme: cosmo
pdf:
documentclass: book
docx:
toc: true
toc-depth: 3
crossref:
chapters: true
```
## Session info
```
sessionInfo(package = c("knitr","rmarkdown"))
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
character(0)
other attached packages:
[1] knitr_1.41 rmarkdown_2.18
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 grDevices_4.2.2 ps_1.7.2 digest_0.6.30 later_1.3.0 jsonlite_1.8.3
[7] evaluate_0.18 datasets_4.2.2 rlang_1.0.6 utils_4.2.2 cli_3.4.1 rstudioapi_0.14
[13] graphics_4.2.2 base_4.2.2 tools_4.2.2 yaml_2.3.6 xfun_0.35 fastmap_1.1.0
[19] compiler_4.2.2 processx_3.8.0 stats_4.2.2 htmltools_0.5.3 methods_4.2.2 quarto_1.2
```
I use Quarto 1.2.269.
```
RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 13_0_1) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
```
### 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": "2022-11-23T04:06:37Z",
"creator": "XiangyunHuang",
"is_pull_request": false,
"labels": [
"bug",
"docx"
],
"locked": false,
"milestone": "Future",
"number": 3434,
"state": "open",
"title": "Word format doesn't respect PART and its contents in Quarto Book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3434"
} |
### Bug description
LaTeX math can't be rendered when output is epub format.
### Step 1. Create a Quarto Book followed by RStudio IDE's guides.
### Step 2. Insert some math to `index.qmd`, here are some examples.
```
$y = \beta_0 + \sum_{i=1}^{999}\beta_i x_i$
$$
S_k = \sum_{x=0}^{k} p_x
$$
$$
p_x = \binom{n}{x}p^x(1-p)^{n-x}, \quad x = 0,1,\cdots,n
$$
```
### Step 3. then Render EPUB, and we will see
#### Output from Render Book
<img width="1775" alt="ζͺε±2022-11-23 10 13 00" src="https://user-images.githubusercontent.com/12031874/203457117-cc1bebd3-9d50-465d-b6c4-b56edb271539.png">
#### Output from EPUB Book
<img width="978" alt="ζͺε±2022-11-23 10 14 30" src="https://user-images.githubusercontent.com/12031874/203457225-e09cf99d-da2d-41a3-a713-d6e58b74a056.png">
## My session info
I use **Quarto 1.2.269**. more info about my session, please see
```
sessionInfo(package = c("knitr","rmarkdown"))
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Ventura 13.0.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
character(0)
other attached packages:
[1] knitr_1.41 rmarkdown_2.18
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 grDevices_4.2.2 ps_1.7.2 digest_0.6.30 later_1.3.0 jsonlite_1.8.3
[7] evaluate_0.18 datasets_4.2.2 rlang_1.0.6 utils_4.2.2 cli_3.4.1 rstudioapi_0.14
[13] graphics_4.2.2 base_4.2.2 tools_4.2.2 yaml_2.3.6 xfun_0.35 fastmap_1.1.0
[19] compiler_4.2.2 processx_3.8.0 stats_4.2.2 htmltools_0.5.3 methods_4.2.2 quarto_1.2
```
RStudio 2022.07.2+576 "Spotted Wakerobin" Release (e7373ef832b49b2a9b88162cfe7eac5f22c40b34, 2022-09-06) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 13_0_1) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
### 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": "2022-11-23T02:21:53Z",
"creator": "XiangyunHuang",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3432,
"state": "closed",
"title": "[WARNING] Could not convert TeX math y = \\beta_0 + \\sum_{i=1}^{999}\\beta_i x_i, rendering as TeX ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3432"
} |
### Bug description
Categories in post title banners don't currently wrap on small screens. Instead they always display as a single row even if they exceed the screen width. Currently (v1.2.269) the CSS for categories is:
```css
.quarto-title .quarto-categories {
display: flex;
column-gap: .4em;
padding-bottom: .5em;
margin-top: .75em;
}
```
Adding the following fixes this:
```css
.quarto-title .quarto-categories {
display: flex;
column-gap: .4em;
padding-bottom: .5em;
margin-top: .75em;
flex-wrap: wrap;
row-gap: .5em;
}
```
### 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": 4,
"created_at": "2022-11-23T00:41:02Z",
"creator": "mccarthy-m-g",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3431,
"state": "closed",
"title": "Categories in post title banners don't wrap on small screens",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3431"
} |
Writing a book in Quarto. I'd like to send individual chapters to colleagues for review, but not send them the entire book. I could send everything to a .docx and then delete most chapters, but I wonder whether there is a neater way to do this. Of course, I could copy the chapter and set up a single chapter document, but that seems inelegant. Any suggestions will be appreciated. | {
"assignee": null,
"comments": 2,
"created_at": "2022-11-22T19:26:05Z",
"creator": "hueyrb",
"is_pull_request": false,
"labels": [],
"locked": true,
"milestone": null,
"number": 4494,
"state": "closed",
"title": "output single chapters in Quarto book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4494"
} |
### Bug description
Hi,
I have the code below.
If I try to render it, the altair chart is not rendered.
If I remove the OJS table the chart is rendered.
In the browser console I have these vega errors:
I'm using quarto 1.3.19 in debian 11.
Thank you
### the code
~~~~
---
title: "tmp"
format:
html:
toc-depth: 4
jupyter: python3
---
## OJS
```{ojs}
//| echo: false
data = FileAttachment("tmp-ojs.csv").csv({ typed: true })
Inputs.table(data)
```
## altair
```{python}
#| echo: false
import pandas as pd
import altair as alt
df = pd.read_csv("tmp.csv",keep_default_na=False)
df['year'] = pd.to_datetime(df['year'], format='%Y')
alt.Chart(df).mark_area().encode(
alt.X('year:T', timeUnit = 'year',title='year',axis=alt.Axis(tickCount='year')),
alt.Y('v:Q',axis=alt.Axis(format='%'),title='percentage'),
color='i:N'
)
```
~~~~
### the input files
#### tmp-ojs.csv
```
F,G,C
9470719.0,1688.0,0.0
5459.0,371872.0,0.0
122.0,2.0,12366.0
26.0,17.0,0.0
```
#### tmp.csv
```
year,i,v
2016,F,0.9599716561118586
2016,G,0.0382418519682473
2016,C,0.0012657864805693667
2016,W,1.2161279236855405e-05
2016,S,4.5402109150926846e-05
2016,O,0.00046314205093691
2017,F,0.9598036277704027
2017,G,0.03840420504605933
2017,C,0.0012674079844676141
2017,W,1.5302943039709717e-05
2017,S,4.864511694742162e-05
2017,O,0.0004608111390831794
2018,F,0.959801296858549
2018,G,0.038401570102224676
2018,C,0.001268016048429457
2018,W,1.6519070963395258e-05
2018,S,5.3610972635804244e-05
2018,O,0.0004589869471976511
2019,F,0.9598036277704027
2019,G,0.03840420504605933
2019,C,0.0012674079844676141
2019,W,1.5302943039709717e-05
2019,S,4.864511694742162e-05
2019,O,0.0004608111390831794
```
### 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": "2022-11-22T12:15:45Z",
"creator": "aborruso",
"is_pull_request": false,
"labels": [
"bug",
"wontfix"
],
"locked": false,
"milestone": null,
"number": 3424,
"state": "closed",
"title": "Impossible to render both Observable table and altair chart",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3424"
} |
### Bug description
I want to re-use sections between different webpages on my website.
Following #3409 discussion, and in light of @dragonstyle's [answer](https://github.com/quarto-dev/quarto-cli/discussions/3409#discussioncomment-4195544), I went ahead and tried quarto's _include_ feature in a Quarto **_website_**.
**Problem:** I cannot render the website. It throws an error:
> ERROR: Include directive failed.
> ...
> could not find file ...
Details About System
---
Quarto version: 1.2.269
<details>
<summary>Session Info</summary>
``` r
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.2.2 (2022-10-31 ucrt)
#> os Windows 8.1 x64 (build 9600)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.1252
#> ctype English_United States.1252
#> tz Asia/Jerusalem
#> date 2022-11-22
#> pandoc 2.19.2 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> - Packages -------------------------------------------------------------------
#> package * version date (UTC) lib source
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
#> digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.1)
#> evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.2)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.2)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.2)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.2)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
#> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
#> rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.2)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.2)
#> 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)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
#> xfun 0.34 2022-10-18 [1] CRAN (R 4.2.2)
#> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.1)
#>
#> [1] C:/Program Files/R/my_packages
#> [2] C:/Program Files/R/R-4.2.2/library
#>
#> ------------------------------------------------------------------------------
```
</details>
Reproducible Example
---
### [A github repo](https://github.com/emmansh/test-quarto-include) with all the files from below.
### Step-by-step to reproduce the bug
#### 1. Create quarto website
1. RStudio -> File -> New Project -> New Directory -> Quarto Website
<img width="268" alt="1" src="https://user-images.githubusercontent.com/18688877/200161174-5a5d2710-8652-408b-b74d-aa9a73084547.png">
#### 2. Set up two separate folders for blog posts & posts themselves
```shell
touch posts_bar.qmd
touch posts_foo.qmd
mkdir posts_bar
mkdir posts_foo
touch posts_bar/post_topic_a.qmd
touch posts_foo/post_topic_b.qmd
```
#### 3. Within files
##### _quarto.yml
```yml
project:
type: website
website:
title: "test-quarto-include"
navbar:
left:
- href: index.qmd
text: Home
- about.qmd
- posts_bar.qmd
- posts_foo.qmd
format:
html:
theme: cosmo
css: styles.css
toc: true
editor: visual
```
##### posts_bar.qmd
```yml
---
title: "Posts Bar"
listing:
contents: posts_bar
type: grid
sort: "date desc"
categories: true
---
```
##### posts_foo.qmd
```yml
---
title: "Posts Foo"
listing:
contents: posts_foo
type: grid
sort: "date desc"
categories: true
---
```
##### post_topic_a.qmd
<pre>
---
title: "Topic A"
---
# Intro
This posts discusses topic A, which is very interesting.
# Code Example
Here is some code about topic A:
```{r}
paste("a", "a", "a", sep = "_")
```
# Summary
Topic A is the most intriguing subject on Earth
</pre>
##### post_topic_b.qmd
<pre>
---
title: "Topic B"
---
# Intro
This posts discusses topic B, which is boring.
# Should we borrow content from other topics?
Let's bring over some content about topic A, which is known to be interesting.
Specifically, there's a section with some code, which I believe is super cool.
Let's use Quarto's `include` feature:
(will it render?)
{{< include /posts_bar/post_topic_a.qmd#code-example >}}
What if we try using underscore in filename?
(will it render?)
{{< include /posts_bar/_post_topic_a.qmd#code-example >}}
</pre>
### 4. Render website & Error
In RStudio -> Build -> Render Website
<br>
<details>
<summary>Log from "Background Jobs" π</summary>
```
Rendering:
[1/6] about.qmd
processing file: about.qmd
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: about.knit.md
[2/6] index.qmd
processing file: index.qmd
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: index.knit.md
[3/6] posts_bar\post_topic_a.qmd
processing file: post_topic_a.qmd
|....................... | 33%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-1
|......................................................................| 100%
ordinary text without R code
output file: post_topic_a.knit.md
[4/6] posts_bar.qmd
[5/6] posts_foo\post_topic_b.qmd
ERROR: Include directive failed.
in file D:\test-quarto-include\posts_foo\post_topic_b.qmd,
could not find file D:\test-quarto-include\posts_bar\post_topic_a.qmd#code-example.
```
</details>
| {
"assignee": null,
"comments": 4,
"created_at": "2022-11-22T09:51:13Z",
"creator": "emmansh",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3421,
"state": "closed",
"title": "`{{< include >}}` in a Quarto website to re-use content between pages throws an error: `Include directive failed... could not find file ...`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3421"
} |
It can't _only_ be solved with an anchor because we need javascript to switch tabs. But it might be possible to add something to our tabby runtime to do this.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3415
<div type='discussions-op-text'>
<sup>Originally posted by **aborruso** November 21, 2022</sup>
Hi,
imagine I have a 3 tabs tabset.
Is there a way to have an anchor link that scroll to that tabset, and open the third?
Thank you</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-11-21T23:01:17Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.4",
"number": 3416,
"state": "open",
"title": "HTML output: is there a tabset anchor?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3416"
} |
### Bug description
When trying to use an extension theme for a revealJS presentation that attempts to `@include` additional `.scss` files, quarto throws an error that it can't find the styles to import when trying to compile the scss.
Reproducible example available in [this repo](https://github.com/dgkf/quarto-revealjs-theme-reprex).
In short, using the same extension, using `format: custom-html` works just fine while `format: custom-revealjs` results in an scss compilation error:
```
ERROR: Theme file compilation failed:
Error: Can't find stylesheet to import.
β·
46 β @import "scss/variables";
β ^^^^^^^^^^^
β΅
```
Tested on current development and latest release of `quarto-cli` on an M1 mac.
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-11-21T19:31:01Z",
"creator": "dgkf",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3414,
"state": "closed",
"title": "Extension themes with @import scss rule fail to compile for revealJS ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3414"
} |
I'm running quarto on MacOS Monterey (12.1).
When issueing the render command I get the following error:
ERROR: TypeError: Cannot read properties of undefined (reading 'toLowerCase').
I've tried rendering from within VSCode and Jupyter Lab. Both give the same error message.
No clue what causes this. | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-21T14:51:19Z",
"creator": "renenadorp",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3411,
"state": "closed",
"title": "ERROR: TypeError: Cannot read properties of undefined (reading 'toLowerCase')",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3411"
} |
If `_quarto.yml` has a part with no chapters, e.g. "Foo" in the example:
```
book:
title: "part-test"
chapters:
- index.qmd
- part: "Foo"
chapters:
- part: "Bar"
chapters:
- "intro.qmd"
```
Then the build fails with:
```
In file _quarto.yml
(line 8, columns 7--11) property name part is invalid
7: - index.qmd
8: - part: "Foo"
~~~~~
9: chapters:
The error happened in location book:chapters:1:part.
```
This is not an issue if building locally where the result renders as expected, with the part "Foo" as a collapsible subheading.
I've [produced a repository](https://github.com/cjdbarlow/part-test) which is a MWE of the issue, both with the correct rendering in `_book` and the github action that prompts the issue.
| {
"assignee": null,
"comments": 5,
"created_at": "2022-11-21T08:08:45Z",
"creator": "cjdbarlow",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3412,
"state": "closed",
"title": "Property name part is invalid when the part is empty and using Github Actions",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3412"
} |
This, in a website, will generate links to `/cv.pdf` and `/blog.html` regardless of the root directory of the website:
````
---
about:
template: trestles
links:
- text: Blog
url: "/blog.html"
- text: CV
url: "/cv.pdf"
---
```` | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-11-20T21:07:11Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3404,
"state": "open",
"title": "root-relative hrefs in template links are not resolved properly",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3404"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3401
<div type='discussions-op-text'>
<sup>Originally posted by **JosiahParry** November 20, 2022</sup>
When including a math expression with `$$ ... $$` they appear immediately and are ignored by incremental options.
tag @cscheid
reprex below
```quarto
---
title: "incremental formulae"
format:
revealjs:
incremental: true
---
# I'm probably doing this wrong
## A slide
- formula 1 (lol)
$$
G = \frac{\sum_{i = 1}^{n} \sum_{j = 1}^{n} w_{ij}x_ix_j}
{\sum_{i = 1}^{n}\sum_{j = 1}^{n} x_i x_j}
$$
- formula 2
$$
Gi = \frac{\sum_j w_{ij} x_j}{\sum_j x_j}
$$
## Another one
:::{.incremental}
- formula 1 (lol)
$$
G = \frac{\sum_{i = 1}^{n} \sum_{j = 1}^{n} w_{ij}x_ix_j}
{\sum_{i = 1}^{n}\sum_{j = 1}^{n} x_i x_j}
$$
- formula 2
$$
Gi = \frac{\sum_j w_{ij} x_j}{\sum_j x_j}
$$
:::
```</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-11-20T15:03:05Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"revealjs"
],
"locked": false,
"milestone": "v1.3",
"number": 3402,
"state": "closed",
"title": "math expressions ignored in incremental slides",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3402"
} |
### Bug description
Hello,
I noticed that for figures and tables generated by a code chunks, Quarto let me reference those by adding a `#| label:` and the relevant label. The same isn't true for equation generated by code chunks.
I would like to display math and equation expressions that actually works in the document, so I'm thinking about using `sympy` or `handcalcs` to display nicely formatted math expression that actually yield results; these equation need to be cross referenceable across the document.
I got a working example where I show the issue using sympy, and a workaround that let me reference a sympy expression by wrapping it in a ``$$...$$` environment, similar to the solution used for displaying pandas dataframe mentioned in the guide.
[equation_label_in_code_chunks.pdf](https://github.com/quarto-dev/quarto-cli/files/10047971/equation_label_in_code_chunks.pdf)
(I would like to attach also the qmd file, but it doesn't seems to be supported by github)
(So I tricked it by changing the extension, just rename it)
[change file extension to qmd.md](https://github.com/quarto-dev/quarto-cli/files/10047974/change.file.extension.to.qmd.md)
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-11-19T21:30:05Z",
"creator": "kompre",
"is_pull_request": false,
"labels": [
"duplicate",
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3397,
"state": "closed",
"title": "use \"#| label: eq-xxx\" to add label to equation generated in code chunks (e.g. sympy) ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3397"
} |
### Bug description
I am trying to to include the render date, time and author email addresses in html reports as in Rmd. For example:
However, I am not able to do that in Quarto, and the time and email just would not show, despite following the instructions here for author information:
https://quarto.org/docs/journals/authors.html
```
title: "Main title in Qmd"
subtitle: "Subtitle"
author:
- name: Adam Smith
affiliation: ABC institute
email: "[email protected]"
```
System:
RStudio 2022.07.2 Build 576, in Windows 10
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-11-19T17:04:59Z",
"creator": "tmss1",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3393,
"state": "closed",
"title": "Author email and time not showing in html reports ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3393"
} |
### Bug description
I am rendering my .qmd files on Mac M2
When I include python code in .qmd files, the following error arises:
```
WARNING: Specified QUARTO_PYTHON '/Users/waterking/opt/anaconda3/bin/python' does not exist.
[1/3] posts/tutorials/ai-course-project.qmd
WARNING: Specified QUARTO_PYTHON '/Users/waterking/opt/anaconda3/bin/python' does not exist.
Starting python3 kernel...ERROR: Error reading kernel transport file: SyntaxError: Unexpected end of JSON input(removing file)
WARNING: Unable to start Jupyter kernel for /Users/websites/my-blog/posts/tutorials/ai-course-project.ipynb
``` | {
"assignee": null,
"comments": 1,
"created_at": "2022-11-19T08:15:21Z",
"creator": "Waterkin",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3391,
"state": "closed",
"title": "ERROR: Error reading kernel transport file: SyntaxError: Unexpected end of JSON input(removing file)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3391"
} |
### Bug description
Using
~~~md
```{r, echo = FALSE}
# INITIALIZE CODE
hello <- 42
```
# Summary
In summary, this book has no content whatsoever.
~~~
in a Quarto Book chapter results in `INITIALIZE CODE` becoming the chapter title used **in the table of content**, although the `Summary` is still the title on the page. See below screenshot.
# Session info
Ubuntu 20.04 with:
```sh
$ quarto --version
1.3.11
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-11-18T20:50:05Z",
"creator": "HenrikBengtsson",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.4",
"number": 3390,
"state": "open",
"title": "Books: Table of Content picks up code-block comments as chapter titles",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3390"
} |
### Bug description
Issue: Any page that is referenced by a sidebar will have that sidebar applied to it, even if a separate definition for that page's sidebar exists in _quarto.yml
Related to https://github.com/quarto-dev/quarto-cli/issues/1853
Observed Behavior: In this repo, observe that the "Get Started" page has a sidebar defined in _quarto.yml and that the "Other" page has zero definition for a sidebar. However, because both are referenced in the sidebar: id: gallery, both of these pages have the sidebar for the Gallery applied.
Expected Behavior: A page will only have the sidebar defined by its sidebar: id.
In this example, I would expect that "Get Started" and "Gallery" would have the sidebars defined by their respective ids and called out by the _metadata.yml file in their directories. I also would expect that "Other" would not have a sidebar.
### Reprex
https://github.com/kmasiello/sidebar-reprex
| {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-11-18T20:41:02Z",
"creator": "kmasiello",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.3",
"number": 3389,
"state": "closed",
"title": "Website hybrid nav - pages referenced by a sidebar will have that sidebar applied to it.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3389"
} |
We have inconsistently rendered descriptions of keyboard shortcuts on the website
- https://quarto.org/docs/get-started/authoring/rstudio.html ("Ctrl-Shift-P")
- https://quarto.org/docs/get-started/computations/rstudio.html ("β§βK")
It would be really slick to have a `keyboard-shortcut` shortcode which rendered a default version of the description on non-interactive formats, but, optionally in javascript formats, sniffed the environment and only showed the os-specific version of the shortcut. | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-11-18T16:57:58Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.3",
"number": 3384,
"state": "closed",
"title": "`keyboard-shortcut` shortcodeΒ ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3384"
} |
The "language content" feature described in the [documentation](https://quarto.org/docs/projects/profiles.html#language-content) doesn't seem to be implemented: rendering the example gives a document with both the English and French quotes.
I think the feature would be bad as default behavior anyway: the `lang` attribute on divs and spans is an established feature in pandoc (unrelated to conditional content), and it's useful in its own right. For example, if I write an English document and add a French paragraph in a div tagged with `{lang=fr}`, for PDF output pandoc will wrap the paragraph in `\begin{otherlanguage}{french}...\end{otherlanguage}` which will apply the correct typographic rules for French.
Maybe this section of the documentation can removed?
Otherwise the feature could be implemented as opt-in behavior? (I agree it can be useful, I actually use `{lang=...}` for conditional content in some projects using a custom Lua filter.) | {
"assignee": "cscheid",
"comments": 2,
"created_at": "2022-11-18T13:53:53Z",
"creator": "knuesel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3372,
"state": "closed",
"title": "Documented \"Language Content\" feature not implemented",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3372"
} |
Where should we set knitr chunk options in YAML? The original proposal from Max was:
```yaml
format:
html:
fig-width: 6
fig-height: 4.25
fig-align: center
```
or
```
knitr:
opts_chunk:
fig-width: 6
fig-height: 4.25
fig-align: center
```
More comments from him:
> Any recommendation? Are there certain options that should go in one place or another?
> Also, I have the equivalent of _common.R. Iβd like to specific device settings there using `knitr::opts_chunk$set(blah blah blah)`
> Does that work too? Iβd use this to alter options based on the target format (i.e. HTML versus LaTeX).
> It looks like dev shouldn't be set in _quarto.yml (and is silently ignored). I set dev: svg for HTML format and it tried to use png.
> My understanding is that some of them can be set under execute in the YAML: https://quarto.org/docs/reference/formats/html.html#execution.
> And some under knitr: https://quarto.org/docs/reference/cells/cells-knitr.html
> And I think instead of dev it's fig-format?
> I'm also curious about the "right" answer to this.
> And I'm fairly certain you can use `knitr::opts_chunk$set(blah blah blah)`.
I (@allenmanning) answered:
> you can use the R code version. also yes its fig-format. The format: html is for universally supported quarto options (i.e. stuff that works in jupyter and knitr). we've attempted to support as much as possible in both but knitr still has a lot of things that jupyter doesn't (thus the opts_chunk failsafe). So I'd say that the correct/recommended approach is to use the universal options (fig-format, execute: echo, etc.) and then only use the opts_chunk for things that are unsupported with the normal syntax
Is there a list of the unsupported options?
we don't currently | {
"assignee": "cwickham",
"comments": 7,
"created_at": "2022-11-18T13:39:12Z",
"creator": "allenmanning",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.4",
"number": 3371,
"state": "open",
"title": "Document unsupported knitr chunk options",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3371"
} |
### Bug description
Dear Quarto Team,
I encountered an annoying bug in Quarto.
To reproduce this bug:
1. create a book with `quarto create project book`
2. put an R chunk producing a figure in one of the chapters
3. set fig-width: 3 and out-width: "85%" in pdf section of format in _quarto.yaml
4. render project
Hope this reports helps to make the software even better :)
Quarto 1.2.269 on Windows 10 (command line)
issue persists after installing Version 1.3.11
````
project:
type: book
book:
title: "repex"
author: "Jane Doe"
date: "18/11/2022"
chapters:
- index.qmd
- intro.qmd
- summary.qmd
- references.qmd
bibliography: references.bib
format:
html:
theme: cosmo
pdf:
documentclass: scrreprt
fig-width: 3
out-width: "85%"
````
````
# Introduction
This is a book created from markdown and executable code.
See @knuth84 for additional discussion of literate programming.
```{r}
#| label: fig-test
#| fig-cap: This is a test
#| echo: false
library(ggplot2)
ggplot(mtcars, aes(x = cyl, y = mpg)) +
geom_violin(aes(group = cyl, colour = factor(cyl)))
```
````
### 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": "2022-11-18T13:29:52Z",
"creator": "fruchtblase",
"is_pull_request": false,
"labels": [
"bug",
"duplicate",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 3370,
"state": "closed",
"title": "out-width is ignored if fig-width is also set in _quarto.yml",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3370"
} |
### Bug description
Hello,
I am trying to switch off the search button in a quarto website project using `search: false`. It does not work in the **navbar**, but works as expected in the **sidebar**.
Thanks, Ahmed
```
project:
type: website
website:
title: ""
navbar:
search: false
format:
html:
theme: cosmo
css: styles.css
toc: true
```
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2022-11-18T12:42:08Z",
"creator": "elgabbas",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 3369,
"state": "closed",
"title": "Can not hide search from a quarto website project's navbar",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3369"
} |
### Bug description
New user here, migrating from fastpages.
I ran `quarto publish` after [migrating my fastpages blog](https://nbdev.fast.ai/tutorials/blogging.html#migrating-from-fastpages), and selected the GitHub Pages deployment option. Despite the [GitHub deployment workflow](https://github.com/drscotthawley/blog_quarto/actions/runs/3494794082) being completed, `quarto publish` seems to be frozen at its final "push":
No CPU usage (from `quarto` or `deno` or `git`) is happening, and there' no outbound network traffic. A look at the [`gh-pages` branch of my repo](https://github.com/drscotthawley/blog_quarto/tree/gh-pages) shows it to be empty.
There is a lot of material to this first commit/publish, however I have waited probably half an hour now, and like I say there is neither CPU activity nor network activity.
Here is a list of the output log:
```
$ quarto publish
? Provider: βΊ GitHub Pages
? Publish site to https://drscotthawley.github.io/blog_quarto/ using gh-pages? (Y/n) βΊ Yes
Switched to a new branch 'gh-pages'
[gh-pages (root-commit) 98a3e04] Initializing gh-pages branch
remote:
remote: Create a pull request for 'gh-pages' on GitHub by visiting:
remote: https://github.com/drscotthawley/blog_quarto/pull/new/gh-pages
remote:
To https://github.com/drscotthawley/blog_quarto.git
* [new branch] HEAD -> gh-pages
Your branch is up to date with 'origin/main'.
Switched to branch 'main'
From https://github.com/drscotthawley/blog_quarto
* branch gh-pages -> FETCH_HEAD
Rendering for publish:
[ 1/35] posts/2020-03-26-Sliding-Off-A-Hill.ipynb
[ 2/35] posts/2017-02-03-How-To-Port-Forward-Jupyter-Notebooks.md
[ 3/35] posts/post-with-code/index.qmd
[ 4/35] posts/2019-02-08-My-1st-NN-Part-3-Multi-Layer-and-Backprop.ipynb
[ 5/35] posts/2021-06-17-Contrasting-Contrastive-Loss.ipynb
WARNING: Malformed Jupyter Output Display Data found:
WARNING: {"model_id":"6256f42ad778484b84c4d61aa8fbddaa","version_major":2,"version_minor":0}
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[11/35] posts/2022-01-24-MultiDim-DotProducts.ipynb
[12/35] posts/2018-02-21-Resolving-OSX-Aliases.md
[13/35] posts/2019-01-30-My-First-Neural-Network.ipynb
[14/35] posts/2020-03-01-Data-Are-Measurements.ipynb
[15/35] posts/2017-05-05-Crash-Course-On-GANs.md
[16/35] posts/welcome/index.qmd
[17/35] posts/2021-02-15-Making-GPT3-Generate-3-Of-A-Kind.md
[18/35] posts/2020-07-01-Citations-Via-Bibtex.md
[19/35] posts/2022-11-17-BYOL.ipynb
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[21/35] posts/2020-12-11-Naughty-by-Numbers.md
[22/35] posts/2018-12-16-Parallelizing-Python-Simplified.md
[23/35] posts/2021-08-06-Live-CL-Demo.md
[24/35] posts/2021-10-15-Geometric-Algebra.ipynb
[25/35] posts/2019-02-04-My-First-NN-Part-2.ipynb
[26/35] posts/2017-11-22-Convexity-Loss-Classification.ipynb
[27/35] posts/2021-05-04-The-Joy-Of-3D-OLD.ipynb
[28/35] posts/2019-12-06-Getting-Started-In-ML-Audio.md
[29/35] posts/2017-05-04-Learning-Room-Shapes.md
[30/35] posts/2020-01-14-test-markdown-post.md
[31/35] posts/2017-02-23-Following-Gravity-Colab.ipynb
[32/35] posts/2017-02-06-Machine-Learning-Reference-List.md
[33/35] posts/2019-12-21-PCA-From-Scratch.ipynb
[34/35] index.qmd
[35/35] about.qmd
Preparing worktree (resetting branch 'gh-pages'; was at 98a3e04)
Branch 'gh-pages' set up to track remote branch 'gh-pages' from 'origin'.
HEAD is now at 98a3e04 Initializing gh-pages branch
[gh-pages 5324814] Built site for gh-pages
206 files changed, 34716 insertions(+)
create mode 100644 .nojekyll
create mode 100644 2017/02/03/How-To-Port-Forward-Jupyter-Notebooks/index.html
create mode 100644 2017/02/06/Machine-Learning-Reference-List/index.html
create mode 100644 2017/02/23/Following-Gravity-Colab/index.html
create mode 100644 2017/05/04/Learning-Room-Shapes/index.html
create mode 100644 2017/05/05/Crash-Course-On-GANs/index.html
create mode 100644 2017/11/22/Convexity-Loss-Classification/index.html
create mode 100644 2018/02/21/Resolving-OSX-Aliases/index.html
create mode 100644 2018/12/16/Parallelizing-Python-Simplified/index.html
create mode 100644 2019/01/30/My-First-Neural-Network/index.html
create mode 100644 2019/02/04/My-First-NN-Part-2/index.html
create mode 100644 2019/02/08/My-1st-NN-Part-3-Multi-Layer-and-Backprop/index.html
create mode 100644 2019/12/06/Getting-Started-In-ML-Audio/index.html
create mode 100644 2019/12/21/PCA-From-Scratch/index.html
create mode 100644 2020/01/13/Mac-Linux-Switch-Notes/index.html
create mode 100644 2020/07/01/Citations-Via-Bibtex/index.html
create mode 100644 2020/11/01/Interactivity_Test/index.html
create mode 100644 2020/12/11/Naughty-by-Numbers/index.html
create mode 100644 2021/08/06/Live-CL-Demo/index.html
create mode 100644 2021/09/15/Handy-Bash-Functions/index.html
create mode 100644 2021/10/15/Geometric-Algebra/index.html
create mode 100644 2022/01/24/MultiDim-DotProducts/index.html
create mode 100644 2022/02/15/Data-Identity/index.html
create mode 100644 2022/11/15/MultiDim-Shells/index.html
create mode 100644 2022/11/17/BYOL/index.html
create mode 100644 about.html
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create mode 100644 posts/2019-12-06-Getting-Started-In-ML-Audio.html
create mode 100644 posts/2019-12-21-PCA-From-Scratch.horigin https://github.com/drscotthawley/blog_quarto.git (fetch)
origin https://github.com/drscotthawley/blog_quarto.git (push)
<frozen for 20 minutes>
```
"Please include a minimal, fully reproducible example in a single .qmd file?" Sorry I don't know what a .qmd file is. But I've included a full output log above.
No using RStudio IDE.
Running on Mac Os Monterey, 12.3
### 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": 25,
"created_at": "2022-11-18T07:18:21Z",
"creator": "drscotthawley",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"publishing"
],
"locked": false,
"milestone": "v1.3",
"number": 3368,
"state": "closed",
"title": "quarto publish frozen at push, web page 404's. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3368"
} |
Not sure if this is a quarto issue, reticulate issue, documentation issue or just plain user error.
Your docs suggest that if (in RStudio) I make an environment with venv in my project directory, this should be picked up automatically by R when I run a python chunk. This is not the case for me; it just loads my last reticulate environment from a previous project, even though the `env` folder is in the project dir.
To fix this, I followed the instructions [here](https://github.com/rstudio/reticulate/issues/292#:~:text=Sys.setenv(RETICULATE_PYTHON%20%3D%20%22/home/superuser/anaconda3/envs/pyres/bin/python%22)) to point my project to the version of python in my `env` folder. Like I said, I'm not 100% sure whether this is an issue with quarto, reticulate, just user error, or something that needs clarification in the docs, but in any case the process was not as straightforward as I expected from reading the docs. | {
"assignee": null,
"comments": 8,
"created_at": "2022-11-17T17:11:58Z",
"creator": "rsenft1",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 4504,
"state": "closed",
"title": "Reticulate does not find venv env/ if previous environment exists",
"url": "https://github.com/quarto-dev/quarto-cli/issues/4504"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3362
<div type='discussions-op-text'>
<sup>Originally posted by **robertwelz** November 17, 2022</sup>
Hi,
i wanted to deploy a website (created with quarto) using QuartoPub using the `quarto publish quarto-pub.` command. I believe i followed all steps in the documentation carefully, but when i publish the website, it only shows a "Page not found" error. I even deleted the old project and started a new website-project from scratch but without success. Here is the link to the website:
[https://robertwelz.quarto.pub/mockwebsite_statistics/](https://robertwelz.quarto.pub/mockwebsite_statistics/)
If i can provide more information to solve this problem, please let me know. I'm a total beginner in this.
Thanks
Robert
</div> | {
"assignee": "softwarenerd",
"comments": 10,
"created_at": "2022-11-17T15:20:32Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug",
"publishing"
],
"locked": false,
"milestone": "v1.4",
"number": 3365,
"state": "open",
"title": "quarto publish quarto-pub put user sites in bad state",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3365"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3359
<div type='discussions-op-text'>
<sup>Originally posted by **fuhrmanator** November 16, 2022</sup>
I spent several hours trying to track down why my CI for the Quarto book project I have (running on ubuntu) wasn't building a valid PDF (there was no error in the build). I had made some big changes to my book project and hadn't verified the PDF on the web, and thought it was I who "broke" things with ubuntu (I actually didn't realize the CI was running the release candidate builds). The PDF was coming out corrupt. I tried to remove all the changes I'd made in the past week, but couldn't get a MWE; the simplest book (hello world preface) was still a corrupt PDF.
On my Windows station everything is OK. I'm using Quarto 1.2.233, and the PDFs are fine. So, when I realized the CI builds were moving ahead of my windows version, I set them to 1.2.233 also, and now everything is OK.
I suspect it has something to do with `pdf-engine: latexmk`, since on a separate laptop I can get a Quarto project to render good PDFs if I don't use `latexmk` with the latest (1.2.269). It looks like some kind of regression (not sure when this started, sorry).</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-11-17T14:05:50Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 3364,
"state": "closed",
"title": "Debugging corrupted PDFs turns out to be a problem with Quarto after 1.2.233 with latexmk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3364"
} |
### Bug description
I am trying to publish quarto-content to a server hosting RStudio Connect. When i run `quarto publish connect inst/quarto.qmd --token $API_KEY --server $CONNECT_SERVER` i get the following error :
```
ERROR: TypeError: error sending request for url (<CONNECT_SERVER>/__api__/v1/content): error trying to connect: invalid peer certificate contents: invalid peer certificate: UnknownIssuer
```
However, when I instead do a curl to the same url (`curl -H "Authorization: Key $API_KEY" ${CONNECT_SERVER}/__api__/v1/content`), I get a valid response with all the contents listings from my RStudio Connect server.
I have checked my certificates from where I run the `quarto publish` command and I do have a valid certificate for the server running RStudio Connect. Additionally, I am able to use [rsconnect-python](https://docs.posit.co/rsconnect-python/), to deploy a .qmd file using manifest.
Any idea why Quarto is unable to communicate with my server running RStudio Connect?
VERSIONS:
- Quarto: version 1.1.251
- OS: Red Hat Enterprise Linux Server version 7.9.
- RStudio Connect: v2022.09.0
### 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": null,
"comments": 3,
"created_at": "2022-11-17T11:44:03Z",
"creator": "TheisFerre",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 3363,
"state": "open",
"title": "Quarto publish connect BadCertificate",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3363"
} |
### Bug description
When rendering two figures created with Julia Plots (GR backend) side-by-side, the font of the plots is tiny. Is there a way to adjust this or is this a bug?
MWE Quarto document is shown below and screenshot demonstrating the problem is attached.
Versions:
Quarto: 1.2.269
OS: macOS 13.0.1
Julia: 1.8.2
Any help is greatly appreciated.
````
---
format:
html:
code-fold: true
output: false
theme: cosmo
jupyter: julia-1.8
---
# Test to demonstrate tiny font for side by side plots
```{julia}
#| output: true
#| fig-cap: Caption
#| fig-subcap:
#| - "Subcaption 1"
#| - "Subcaption 2"
#| layout-ncol: 2
using Plots
p1 = plot(rand(4,2))
p2 = plot(rand(6,2))
display(p1)
display(p2)
```
````
### 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": "2022-11-17T04:51:26Z",
"creator": "plessl",
"is_pull_request": false,
"labels": [
"bug",
"julia"
],
"locked": false,
"milestone": null,
"number": 3361,
"state": "closed",
"title": "Tiny font for side-by-side plot",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3361"
} |
### Bug description
<img width="958" alt="render-pdf_open-in-browser" src="https://user-images.githubusercontent.com/20233085/202265650-f31857fe-c785-4506-99e3-2605a49c593f.png">
'Open in Browser' opens https://coder.jupyter.b-data.ch/hub/proxy/7095/web/viewer.html, which is wrong.
---
<img width="958" alt="render-pdf_browse-at" src="https://user-images.githubusercontent.com/20233085/202265934-2a898c15-23d0-4d90-8133-19f3ce67c659.png">
Browse at shows https://coder.jupyter.b-data.ch/user/benz0li/code-server/proxy/7095/web/viewer.html, which is correct.
---
@jjallaire @cscheid @dragonstyle May be reproduced at https://coder.jupyter.b-data.ch with image `R (jupyterlab/r/verse:latest-devtools)` using
````qmd
---
title: "ggplot2 demo"
author: "Norah Jones"
date: "5/22/2021"
format:
html:
code-fold: true
fig-format: svg
---
## Air Quality
@fig-airquality further explores the impact of temperature on ozone level.
```{r}
#| label: fig-airquality
#| fig-cap: Temperature and ozone level.
#| warning: false
library(ggplot2)
ggplot(airquality, aes(Temp, Ozone)) +
geom_point() +
geom_smooth(method = "loess"
)
```
````
### 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.
- [ ] 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": 7,
"created_at": "2022-11-16T18:55:07Z",
"creator": "benz0li",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3352,
"state": "closed",
"title": "Render PDF: 'Open in Browser' opens wrong link (code-server with Jupyter Server Proxy)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3352"
} |
### Bug description
Hello. Getting an error which I've failed to find any help online for. Hoping someone can advise please? I can't render a very simple quarto page. See below. I'm using vs code on Windows.
```
PS C:\Users\u1191972\Desktop\projects\global-risk-scores> quarto preview cc_approach.qmd --to pdf --no-browser --no-watch-inputs watch-inputs
processing file: cc_approach.qmd
| | |
|.............. | 2
| 20%
ordinary text without R code | 40%
| |............................
| 40% | 60%
label: unnamed-chunk-1
| |..........................................
| 60%
ordinary text without R code | 80%
| |........................................................
| 80%
label: unnamed-chunk-2 (with options)
List of 1
$ engine: chr "python"
Quitting from lines 12-13 (cc_approach.qmd)
Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
object 'wrap' not found
Calls: .main ... <Anonymous> -> wrap -> yoink -> do.call -> ::: -> get
Execution halted
```
Everything seems ok though?
```
quarto check
[>] Checking Quarto installation......OK
Version: 1.2.269
Path: C:\Users\u1191972\AppData\Local\Programs\Quarto\bin
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.8.8
Path: C:/Users/u1191972/AppData/Local/Programs/Python/Python38/python.exe
Jupyter: 4.9.1
Kernels: python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.0.2
Path: C:/PROGRA~1/R/R-40~1.2
LibPaths:
- C:/Users/u1191972/R_Library
- C:/Program Files/R/R-4.0.2/library
rmarkdown: 2.5
[>] Checking Knitr 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.
- [ ] 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": 5,
"created_at": "2022-11-16T15:45:54Z",
"creator": "JimShady",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 3351,
"state": "closed",
"title": "Quarto will not render - object 'wrap' not found",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3351"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/3349
<div type='discussions-op-text'>
<sup>Originally posted by **aghaynes** November 16, 2022</sup>
According to the help files for mermaid, it is possible to have invisible links between nodes in mermaid charts, which can be particularly useful for enforcing a particular layout. https://mermaid-js.github.io/mermaid/#/flowchart?id=an-invisisble-link E.g. the following code should produce the flowchart further down.
````
```{mermaid}
flowchart LR
box1 --> box2
box2 --- box3
box4 ~~~ box2
```
````
Executing the chunk in quarto produces a syntax error though.
It seems like the invisible links are probably a new feature (there's an issue referencing a commit in mid-October - https://github.com/mermaid-js/mermaid/issues/3192).
I guess this would require an update to the version of mermaid in quarto?</div> | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-11-16T13:17:39Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"mermaid"
],
"locked": false,
"milestone": "v1.3",
"number": 3350,
"state": "closed",
"title": "Invisible links in mermaid",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3350"
} |
### Bug description
## Bug Description
While running quarto preview from within a Docker container on my M1 Mac, I am not served a localhost URL for the preview. Here is my output which *appears* to run fine.
```
$ quarto preview index.qmd
pandoc
to: html
output-file: index.html
standalone: true
title-prefix: EDoN Secure Research Environment Wiki
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
css:
- styles.css
toc: false
metadata
pagetitle: EDoN Secure Research Environment Wiki
document-css: false
link-citations: true
date-format: long
lang: en
theme:
- sandstone
- custom.scss
```
But as mentioned I was expecting a localhost URL output in the terminal.
*Note* everything is fine when running on my M1 Mac locally.
and here is my Dockerfile:
```dockerfile
FROM rocker/r-ver:4.2.1
RUN apt-get update
RUN apt-get install -y --no-install-recommends libxt6
RUN apt-get install nano
RUN apt-get install -y libxml2 libodbc1
ENV S6_VERSION=v2.1.0.2
ENV RSTUDIO_VERSION=2022.07.2+576
ENV DEFAULT_USER=rstudio
ENV PANDOC_VERSION=default
ENV QUARTO_VERSION=1.2.269
RUN /rocker_scripts/install_rstudio.sh
RUN /rocker_scripts/install_pandoc.sh
RUN /rocker_scripts/install_quarto.sh
RUN quarto install extension --no-prompt quarto-ext/grouped-tabsets
RUN useradd -u 1001 -g rstudio -m conda
RUN useradd -u 504 -g rstudio -m mac
USER conda
WORKDIR /home/conda
ENV PATH="/home/conda/miniconda3/bin:${PATH}"
ARG PATH="/home/conda/miniconda3/bin:${PATH}"
ENV MLFLOW_BIN=/home/conda/miniconda3/bin/mlflow
ENV MLFLOW_PYTHON_BIN=/home/conda/miniconda3/bin/python
RUN wget \
https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
&& bash Miniconda3-latest-Linux-x86_64.sh -b \
&& rm -f Miniconda3-latest-Linux-x86_64.sh
RUN conda --version
USER root
RUN R -q -e 'install.packages(c("reticulate","vetiver","pins","dplyr","checkmate","quarto","gt","tidymodels","randomForest","tidyverse","lcmm"))'
ENV PATH "$PATH:/root/.local/share/r-miniconda/bin"
RUN R -q -e 'reticulate::py_install(envname="base",c("vetiver","pins","scikit-learn","pandas","nbformat","nbclient"),pip=TRUE)'
ENV USER="rstudio"
CMD ["/usr/lib/rstudio-server/bin/rserver", "--server-daemonize", "0", "--auth-none", "1"]
EXPOSE 8787
CMD ["/init"]
```
I have also tried manually specifiy the port in the_quarto.yml file, but I get a "refused to connect" error when opening `http://localhost/4200` in my browser.
```
project:
type: website
output-dir: docs
preview:
port: 4200
browser: false
resources:
- "get-started/new-cars.csv"
render:
- about.qmd
- index.qmd
- learn-more/*
- get-started/index.qmd
- get-started/version.qmd
- get-started/monitor.qmd
- learn-more/containers.qmd
```
## Steps to reproduce
```
git clone https://gitlab.com/arronlacey/r_miniconda_container.git
cd r_miniconda_container
git pull registry.gitlab.com/arronlacey/r_miniconda_container
docker run --rm -p 8787:8787 -v ${PWD}:/mnt registry.gitlab.com/arronlacey/r_miniconda_container
docker exec -it <image name> /bin.bash
cd /mnt
quarto preview index.qmd
```
## System info
macOS Monterey 12.5.1
quarto 1.2.269
### 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": 5,
"created_at": "2022-11-16T11:46:48Z",
"creator": "arronlacey",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"third-party"
],
"locked": false,
"milestone": null,
"number": 3346,
"state": "closed",
"title": "quarto fails to preview from inside a docker image that is running on M1 Mac",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3346"
} |
### Bug description
What am I doing wrong? Is there a way to get quarto to recognize the python path without reinstalling python?
OS: Windows 10
Quarto: 1.3.7
Python 3.8.6
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
Running quarto check gives the following:
```
k:\quarto>quarto check
[>] Checking Quarto installation......OK
Version: 1.3.7
Path: k:\quarto\bin
CodePage: 65001
[>] Checking basic markdown render....OK
WARNING: Specified QUARTO_PYTHON 'k:\python\App\Python;' does not exist.
[>] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[>] Checking R installation...........OK
Version: 4.2.2
Path: k:/R-Portable/App/R-Portable
LibPaths:
- k:/R-Portable/App/R-Portable/library
rmarkdown: 2.18
[>] Checking Knitr engine render......OK
```
The directory containing the python exe:
```shell
Directory of k:\python\App\python
11/16/2022 01:24 PM <DIR> .
11/16/2022 01:24 PM <DIR> ..
01/03/2021 06:48 PM <DIR> DLLs
01/03/2021 06:48 PM <DIR> Doc
07/17/2021 12:54 PM <DIR> etc
04/08/2021 12:23 PM <DIR> include
01/03/2021 06:49 PM <DIR> Lib
01/03/2021 06:49 PM <DIR> libs
09/23/2020 04:00 PM 32,622 LICENSE.txt
02/21/2021 08:36 AM <DIR> man
09/23/2020 04:00 PM 924,374 NEWS.txt
09/23/2020 04:00 PM 100,368 python.exe
09/23/2020 04:00 PM 58,896 python3.dll
09/23/2020 04:00 PM 4,205,584 python38.dll
09/23/2020 04:00 PM 98,832 pythonw.exe
05/21/2022 12:52 PM <DIR> Scripts
07/17/2021 12:56 PM <DIR> share
01/03/2021 06:49 PM <DIR> tcl
01/03/2021 06:49 PM <DIR> Tools
09/23/2020 04:00 PM 101,672 vcruntime140.dll
09/23/2020 04:00 PM 44,328 vcruntime140_1.dll
8 File(s) 5,566,676 bytes
```
### 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": "2022-11-16T09:32:14Z",
"creator": "fortunewalla",
"is_pull_request": false,
"labels": [
"windows"
],
"locked": false,
"milestone": "v1.3",
"number": 3343,
"state": "closed",
"title": "python not detected by `quarto check` but works in cmd & RStudio",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3343"
} |
### Bug description
There is inconsistent behavior when including citation keys inside tables, but it's a really tricky issue and I'm not sure if it's a Quarto issue or an issue with other table-making packages.
When making a table with regular Markdown or with `knitr::kable()`, citation keys that are included in table rows are rendered correctly by pandoc.
However, when making a table with `kableExtra::kbl()` or `gt::gt()`, pandoc doesn't see the citation keys.
Here's a reproducible example:
````
---
title: "Citations in tables"
format: html
references:
- type: article-journal
id: Lovelace1842
author:
- family: Lovelace
given: Augusta Ada
issued:
date-parts:
- - 1842
title: >-
Sketch of the analytical engine invented by Charles Babbage, by LF Menabrea,
officer of the military engineers, with notes upon the memoir by the translator
title-short: Molecular structure of nucleic acids
container-title: Taylorβs Scientific Memoirs
volume: 3
page: 666-731
language: en-GB
---
## Raw Markdown
This works.
| Thing | Citation |
|-------|---------------|
| 1234 | @Lovelace1842 |
## `knitr::kable()`
This works.
```{r}
library(knitr)
tibble::tribble(
~Thing, ~Citation,
1234, "@Lovelace1842"
) |>
kable()
```
## `kableExtra::kbl()`
This doesn't work.
```{r}
library(kableExtra)
tibble::tribble(
~Thing, ~Citation,
1234, "@Lovelace1842"
) |>
kbl() |>
kable_styling()
```
## `gt::gt()`
This doesn't work.
```{r}
library(gt)
tibble::tribble(
~Thing, ~Citation,
1234, "@Lovelace1842"
) |>
gt()
```
````
Raw Markdown and `knitr::kable()` work correctly:
<img width="883" alt="image" src="https://user-images.githubusercontent.com/73663/202052027-f7683db1-cd2b-47ca-86c4-6b1910aed957.png">
`kableExtra::kbl()` and `gt::gt()` do not render the citation:
<img width="753" alt="image" src="https://user-images.githubusercontent.com/73663/202052106-610933bc-b59e-4bc7-af44-dc8bb7bed568.png">
---
This is a known issue in both **kableExtra** (https://github.com/haozhu233/kableExtra/issues/214#issuecomment-421706528) and **gt** (https://github.com/rstudio/gt/issues/112#issuecomment-632936052), and the existing solution for both packages is to use **bookdown**'s text reference feature to render the citation outside of the table and then automatically include the rendered citation inside the table when knitting, like this:
````
(ref:lovelace) @Lovelace1842
```{r}
library(kableExtra)
tibble::tribble(
~Thing, ~Citation,
1234, "(ref:lovelace)"
) |>
kbl() |>
kable_styling()
```
````
This doesn't work in Quarto, though. #1959 and #1785 are about adding bookdown-esque text references to Quarto, which would potentially solve this issue.
---
This is with RStudio 2022.07.2+576 on macOS Monterey 12.6, but it happens across platforms
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 8,
"created_at": "2022-11-16T00:19:10Z",
"creator": "andrewheiss",
"is_pull_request": false,
"labels": [
"bug",
"crossref",
"tables"
],
"locked": false,
"milestone": "v1.4",
"number": 3340,
"state": "open",
"title": "Citations in tables do not render correctly outside of raw markdown and kable",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3340"
} |
### Bug description
Hello,
I am trying to change the values of `code-block-border-left-size`, `code-block-border-left-style` and `max-width`, without success. Do I correctly change them or is this due to a bug?
````
---
format:
html:
code-block-bg: true
code-block-border-left: "#31BAE9"
code-block-border-left-style: "dotted" # no effect
code-block-border-left-size: "10px" # also tried 10px or 10 without quotation
max-width: "1800px" # no effect
---
```{r}
#
1 + 1
```
```{r}
#
2 * 2
```
````
Thanks, Ahmed
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [ ] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": null,
"comments": 4,
"created_at": "2022-11-15T20:17:26Z",
"creator": "elgabbas",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 3337,
"state": "closed",
"title": "Changing `code-block-border-left-size`, `code-block-border-left-style` and `max-width` ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3337"
} |
[WinGet Releaser](https://github.com/vedantmgoyal2009/winget-releaser) is a workflow that automatically creates manfiests for [winget-pkgs](https://github.com/vedantmgoyal2009/winget-releaser) and creates a PR for it. It would look a bit like this:
```yaml
name: Publish to WinGet
on:
release:
types: [released]
jobs:
publish:
runs-on: windows-latest
steps:
- uses: vedantmgoyal2009/winget-releaser@v1
with:
identifier: RStudio.quarto
token: ${{ secrets.WINGET_TOKEN }}
``` | {
"assignee": "cderv",
"comments": 1,
"created_at": "2022-11-15T17:44:39Z",
"creator": "russellbanks",
"is_pull_request": false,
"labels": [
"enhancement",
"windows"
],
"locked": false,
"milestone": "Future",
"number": 3334,
"state": "closed",
"title": "Use WinGet Releaser for automated releases to winget-pkgs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3334"
} |
### Bug description
References to RStudio PBC should be updated to Posit, e.g. https://github.com/quarto-dev/quarto-cli/blob/06f518b480bbd451ccaac466c73b123e9e758e43/COPYRIGHT#L2
### 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": "rich-iannone",
"comments": 0,
"created_at": "2022-11-15T06:02:08Z",
"creator": "philip-khor",
"is_pull_request": false,
"labels": [
"bug",
"documentation"
],
"locked": false,
"milestone": "v1.3",
"number": 3329,
"state": "closed",
"title": "Change RStudio PBC references to Posit",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3329"
} |
### Bug description
I took a json string and escaped it, and it works fine as text embedded inside mermaid (tested using mermaid online https://mermaid.live/), but quarto fails to compile the mermaid graph as part of a slide presentation.
```
graph TD
A["{"a":2, <br/> "b":3, <br/> "d":"b"}"] -->|jq| B(Go shopping)
B --> C{Let me think}
```
graph TD
A["{"a":2, <br/> "b":3, <br/> "d":"b"}"] -->|jq| B(Go shopping)
B --> C{Let me think}
<img width="224" alt="image" src="https://user-images.githubusercontent.com/68746303/201810969-15d7817b-6358-43d3-9a27-a2291f880267.png">
2022.07.2 Build 576
### Checklist
- [X] Please include a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] Please [format your issue](https://quarto.org/bug-reports.html#formatting-make-githubs-markdown-work-for-us) so it is easier for us to read the bug report.
- [X] Please document the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] Please document the operating system you're running. If on Linux, please provide the specific distribution. | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-11-15T02:24:17Z",
"creator": "bayeslearner",
"is_pull_request": false,
"labels": [
"bug",
"needs-repro",
"mermaid"
],
"locked": false,
"milestone": "v1.3",
"number": 3328,
"state": "closed",
"title": "No way to escape special characters in mermaid embedded in quarto docs. ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/3328"
} |
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