page_content
stringlengths 0
46.9k
| metadata
dict |
|---|---|
I often find myself emailing Rmarkdown reports rendered in HTML to collaborators. I recently tried this with an HTML file rendered from a Quarto document. It renders correctly but after I email the document all the plots do not display and instead are replaced by an icon of a broken image.
This has happened with Quarto documents in a regular R project and a Quarto project. I have tried it on Windows and Mac. I have tried emailing through my work email (Microsoft Outlook) and personal Gmail.
Minimal reproducible example below:
````
---
title: "test"
format: html
---
```{r}
x <- rlnorm(1000, 3, 0.3)
hist(x)
```
````
Rendered document before email:
Rendered document after email:
R session info:
`R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0 knitr_1.37 xfun_0.29 `
| {
"assignee": null,
"comments": 3,
"created_at": "2022-08-10T15:45:01Z",
"creator": "mzobeck",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1877,
"state": "closed",
"title": "plots break when i email Quarto html files",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1877"
} |
We should audit our schemas and code for places where we expect an image, and replace what's currently a `string` with a
```yaml
- name: image
schema:
anyOf:
- string
- object:
properties:
src: path
alt: string
required:
- src
```
We should also have a typescript type that matches the schema, and then have our code treat these uniformly, including tracking the alt text automatically. | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-08-10T14:53:13Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"yaml-validation"
],
"locked": false,
"milestone": "v1.4",
"number": 1794,
"state": "open",
"title": "Use \"image\" schema",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1794"
} |
### Bug description
I've just started using quarto and decided to convert an old `LaTeX` book into a new quarto document and have started the process of learning and translating. I'm come across what I think is strange behaviour for the html output.
I have a series of figures that were compiled from `tikz` documents into PDF files and I want to include this pdfs as images.
I assume that the simple figure syntax would also work for pdfs so I've added the figure as:
```md
{#fig-bondContactRadius}
```
and this is generated as:
I'm not sure why the figure is a) rendered so small and b) seems to be in some scrolling window. Is there something special needed to include pdf files as images?
I'm using VS Code on windows if that matters.
### `quarto check` Output
```bash
>quarto check
Kernels: julia-1.4, julia-1.6, julia-1.7, juliapro_v1.5.4-1-1.5, pycharm-20203b08, python3, iota
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.1.3
Path: C:/PROGRA~1/R/R-41~1.3
LibPaths:
- C:/Users/xxx/Documents/R/win-library/4.1
- C:/Program Files/R/R-4.1.3/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
>quarto tools check
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
D:\Workspace\quarto\book>
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 5,
"created_at": "2022-08-10T14:12:20Z",
"creator": "jpmorr",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1791,
"state": "closed",
"title": "Add PDF as image leads to unexpected html output in quarto book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1791"
} |
### Bug description
`mainfont`, `monofont`, `fontsize`, `linestretch`, and `monobackgroundcolor` are listed as [YAML header options](https://quarto.org/docs/reference/formats/presentations/revealjs.html) for Revealjs presentations, but they are ignored when the presentation is rendered - only shows the defaults for these theme elements.
System is Mac OS X (Big Sur 11.6.8) with the latest RStudio Preview release (22.07.01 Build 554) and the latest Quarto release (1.0.38). The full test Quarto document is:
````md
---
title: "Test"
format:
revealjs:
mainfont: "Times New Roman"
monofont: "Times New Roman"
fontsize: "10px"
linestretch: 5
monobackgroundcolor: green
---
## Hello, World!
Hello, world!
```{r}
#| echo: true
print("Hello, world!")
```
````
The (no format change) result is the same for any option in isolation or in combination. But the YAML header options work fine if the format is switched to `html`.
I can make all these format changes just fine using a Sass theme - so the question is not how to make these changes, but rather whether or not they should work using the YAML header options.
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.38
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.7
Path: /Users/ryan/.pyenv/versions/3.9.7/bin/python3
Jupyter: 4.11.1
Kernels: julia-0.4, ir, julia 0.3, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-08-10T13:59:00Z",
"creator": "ryanraaum",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1790,
"state": "open",
"title": "YAML font options ignored for revealjs presentations",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1790"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1780
<div type='discussions-op-text'>
<sup>Originally posted by **chrizz89** August 10, 2022</sup>
I am considering transitioning from latex to quarto for my current project. One thing I have not been able to get going is **making use of the latex glossaries package in quarto**. It does work as far as commands (which rely on my definitions inside `glossary.tex`) are processed and displayed correctly but **printing my glossary does absolutly not work**.
I have tried `keep-tex: true`as well as `latex-clean: false` as my web search suggests it has some thing todo with glossaries requiring multiple latex compilations in order to work, but non if it seemed to work so far. (I tried pdflatex as well as xelatex for rendering)
Any suggestions how to tackle this?
as small example how I implemented it in my _quarto.yml:
```
format:
pdf:
documentclass: scrbook
include-in-header:
- \usepackage[acronym, nonumberlist]{glossaries}
- \makeglossaries
include-before-body:
- \input{glossary.tex}
include-after-body:
- \printglossary[type=\acronymtype]
keep-tex: true
latex-clean: false
latex-min-runs: 3
```
</div> | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-08-10T11:43:28Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.3",
"number": 1782,
"state": "closed",
"title": "how to tweak quarto render process to be compatible w/ latex glossaries package?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1782"
} |
### Bug description
Syntax to insert display style math equations in Quarto documents does not follow conventions explained in the [math section of Pandoc user manual](https://pandoc.org/MANUAL.html#math).
This issue does not affect inline math expressions and it is probably related to issue report #1181, currently in progress.
This is a minimal reproducible example: https://gist.github.com/glimmerphoenix/641d5e35d7194abadb721c0d9b1e14f2.
In summary:
- Math delimiter for display style expressions must be `$$ ... $$` and preferably written in the same line as the math equation.
- The following option documented in the Pandoc user manual does not work in Quarto:
> In this case, the delimiters may be separated from the formula by whitespace.
- The parser still works after invalid inline math expressions, but stops working after the first display style math expression with incorrect syntax. Not sure if this is due to Quarto or Pandoc internal conversion.
- Finally, the recommended syntax for Quarto math expressions described in #1181, suggesting to leave each `$$` delimiter in a separate line, is valid according to Pandoc documentation but does not follow the standard syntax for document convertion. In fact, as I have commented in #1181, both syntax alternatives (`$$` in same line vs. `$$` in a separate line) cannot be mixed in the same document, since the parser stops working at all.
**OS and packages info**
- Platform: Linux, Ubuntu 20.04
- R: 4.2.1
- RStudio: 2022.07.1 Build 554
- Quarto: 1.0.38
- quarto CRAN package: 1.2
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.38
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.10
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
There is an unactivated Python environment in miniconda3. Did you forget to activate it?
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib/R
LibPaths:
- /home/jfelipe/R/x86_64-pc-linux-gnu-library/4.2
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 5,
"created_at": "2022-08-10T10:08:17Z",
"creator": "glimmerphoenix",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1781,
"state": "closed",
"title": "Display style math syntax not compliant with Pandoc documentation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1781"
} |
# User story
As a researcher, I want to have an integration with academic writing platform so that I can collaborate with researchers not using Quarto.
## Academic writing platform
One of the academic writing platform I wish to suggest is Sciflow. They are open source, the document are XML-based and interoperable. AFAIK, they can import markdown files, thus (should be) easing the integration with Quarto.
## Impact
This will expedite the process of collaborative scientific reporting, especially in fields where reproducible report using Quarto is not a thing (yet). | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-10T07:18:01Z",
"creator": "lamurian",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1777,
"state": "open",
"title": "Integrating the reporting workflow with collaborative academic writing platform (e.g. Sciflow)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1777"
} |
### Bug description
hello,
In office, I have an rdp windows server.
when I open a quarto web project on the local server everything is fine but when I try to open a quarto web project
on another hard drive where data should be stored RStudio fails to create the .yml, .qmd and .css files. only the .Rproj file
is created and there is an error that says the system can not find the file specified.
so, for now we can't use the quarto projects outside the hosting server of the RStudio session.
The server is new and I'm installing everything from scratch, so everything is updated.
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cderv",
"comments": 2,
"created_at": "2022-08-09T23:06:38Z",
"creator": "eviatargu",
"is_pull_request": false,
"labels": [
"bug",
"windows",
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 1774,
"state": "open",
"title": "open a quarto web project on internal network harddrive fails",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1774"
} |
The customizing numbering seems not to work. See more detailed discussion in Q&A #1748 below.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1748
<div type='discussions-op-text'>
<sup>Originally posted by **sammo3182** August 9, 2022</sup>
I was excited about the [custom setting of references](https://quarto.org/docs/authoring/cross-references.html#references-1) but cannot find the correct way to set them. In the example below, I tried to change the section and figure labels to alphabetic and sub labels to roman. But as the screenshot shows, none of the section numbers, figure numbers, or their references changed in either pdf or HTML format. I tried to move `number-sections: true` and/or `crossref` under `pdf`. Nothing changed.
What I hope to get are:
1. Customizing the section, table, and figure numbering and correctly cross-referring them. (#873 discussed this issue, but I wonder if there is an easier way to do this for HTML, pdf, and docx all)
2. Setting the numbering of some sections differently from the previous, for instance, `arabic` for main content sections and `alpha` for appendices. (#1283 post a similar demand but it seems no good solution yet)
````markdown
---
title: "test"
number-sections: true
format:
pdf: default
html: default
crossref:
sec-labels: alpha A
subref-labels: roman i
---
# section
@fig-test
# section {#sec-test1}
## subsection {#sec-test2}
@sec-test1
@sec-test2
# section
# References {.unnumbered}
```{r fig-test}
#| fig-cap: "A plot"
plot(mtcars$mpg)
```
````
</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-09T22:03:42Z",
"creator": "sammo3182",
"is_pull_request": false,
"labels": [
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 1771,
"state": "open",
"title": "Custom Section Numbering Not Functioning",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1771"
} |
### Bug description
I am trying to render a Rmd file that has a long name:
`2020-12-16-dynamic-time-warping-and-hierarchical-clustering-with-gapminder`
But I get this error:
`Error running filter C:/Users/<user-name>/AppData/Local/Programs/Quarto/share/filters/crossref/crossref.lua:
...ocal/Programs/Quarto/share/filters/crossref/crossref.lua:3019: attempt to index a nil value (local 'file')
stack traceback:
...ocal/Programs/Quarto/share/filters/crossref/crossref.lua:2914: in function <...ocal/Programs/Quarto/share/filters/crossref/crossref.lua:2908>`
When I change the file name to `2020-12-16-dtw`, it renders successfully.
## Contents of Rmd file:
```
---
title: Dynamic Time Warping and Hierarchical Clustering with {gapminder}
date: '2020-12-16'
---
Abc
```
### RStudio Version:
2022.07.1 Build 554
### OS:
Windows 10
### Session Info:
```
> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
Random number generation:
RNG: L'Ecuyer-CMRG
Normal: Inversion
Sample: Rejection
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices
[4] utils datasets methods
[7] base
other attached packages:
[1] ggrepel_0.9.1 gapminder_0.3.0
[3] factoextra_1.0.7 dtwclust_5.5.6
[5] dtw_1.22-3 proxy_0.4-25
[7] gganimate_1.0.7 magick_2.7.2
[9] here_1.0.1 forcats_0.5.1
[11] stringr_1.4.0 dplyr_1.0.9
[13] purrr_0.3.4 readr_1.4.0
[15] tidyr_1.2.0 tibble_3.1.7
[17] ggplot2_3.3.6 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] readxl_1.3.1
[2] backports_1.2.1
[3] plyr_1.8.6
[4] sp_1.4-5
[5] crosstalk_1.2.0.9000
[6] digest_0.6.29
[7] foreach_1.5.1
[8] htmltools_0.5.3.9000
[9] viridis_0.5.1
[10] rsconnect_0.8.16
[11] fansi_1.0.3
[12] magrittr_2.0.3
[13] memoise_2.0.1
[14] cluster_2.1.0
[15] doParallel_1.0.16
[16] openxlsx_4.2.3
[17] modelr_0.1.8
[18] extrafont_0.17
[19] RcppParallel_5.0.2
[20] extrafontdb_1.0
[21] pkgdown_1.6.1
[22] prettyunits_1.1.1
[23] colorspace_2.0-1
[24] rvest_1.0.2
[25] haven_2.5.0
[26] xfun_0.31
[27] crayon_1.5.1
[28] jsonlite_1.8.0
[29] bigmemory.sri_0.1.3
[30] iterators_1.0.13
[31] glue_1.6.2
[32] gtable_0.3.0
[33] webshot_0.5.2
[34] car_3.0-10
[35] Rttf2pt1_1.3.8
[36] abind_1.4-5
[37] scales_1.1.1
[38] DBI_1.1.1
[39] rstatix_0.6.0
[40] miniUI_0.1.1.1
[41] Rcpp_1.0.8.3
[42] viridisLite_0.4.0
[43] xtable_1.8-4
[44] progress_1.2.2
[45] clue_0.3-58
[46] foreign_0.8-80
[47] stats4_4.0.3
[48] rayshader_0.24.1
[49] htmlwidgets_1.5.4
[50] httr_1.4.3
[51] modeltools_0.2-23
[52] ellipsis_0.3.2
[53] pkgconfig_2.0.3
[54] farver_2.1.0
[55] dbplyr_2.1.1
[56] utf8_1.2.1
[57] tidyselect_1.1.2
[58] labeling_0.4.2
[59] rlang_1.0.4
[60] manipulateWidget_0.10.1
[61] reshape2_1.4.4
[62] later_1.3.0
[63] munsell_0.5.0
[64] cellranger_1.1.0
[65] tools_4.0.3
[66] cachem_1.0.3
[67] cli_3.3.0
[68] generics_0.1.3
[69] gifski_0.8.6
[70] broom_1.0.0
[71] evaluate_0.15
[72] fastmap_1.1.0
[73] yaml_2.3.5
[74] knitr_1.39
[75] fs_1.5.2
[76] zip_2.2.0
[77] rgl_0.106.8
[78] dendextend_1.14.0
[79] mime_0.12
[80] xml2_1.3.3
[81] flexclust_1.4-0
[82] compiler_4.0.3
[83] rstudioapi_0.13
[84] curl_4.3.2
[85] png_0.1-7
[86] ggsignif_0.6.0
[87] reprex_2.0.1
[88] tweenr_1.0.1
[89] stringi_1.7.8
[90] RSpectra_0.16-0
[91] lattice_0.20-41
[92] Matrix_1.2-18
[93] nloptr_1.2.2.2
[94] shinyjs_2.0.0
[95] ggsci_2.9
[96] vctrs_0.4.1
[97] pillar_1.8.0
[98] lifecycle_1.0.1
[99] data.table_1.13.6
[100] bigmemory_4.5.36
[101] raster_3.4-10
[102] httpuv_1.6.1
[103] R6_2.5.1
[104] promises_1.2.0.1
[105] gridExtra_2.3
[106] rio_0.5.16
[107] codetools_0.2-18
[108] assertthat_0.2.1
[109] rprojroot_2.0.3
[110] withr_2.5.0
[111] parallel_4.0.3
[112] hms_1.1.0
[113] grid_4.0.3
[114] class_7.3-17
[115] rmarkdown_2.14
[116] carData_3.0-4
[117] ggpubr_0.4.0
[118] shiny_1.6.0
[119] lubridate_1.8.0
```
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.38
Path: C:\Users\umair\AppData\Local\Programs\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.10.2
Path: C:/Python310/python.exe
Jupyter: 4.9.2
Kernels: julia-1.5, python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.1.3
Path: C:/PROGRA~1/R/R-41~1.3
LibPaths:
- C:/Users/umair/Documents/R/win-library/4.1
- C:/Program Files/R/R-4.1.3/library
rmarkdown: 2.13
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[>] Inspecting toolso.cmd tools check
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Up to date v2022.08 v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 12,
"created_at": "2022-08-09T21:59:59Z",
"creator": "durraniu",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1770,
"state": "closed",
"title": "Error running filter crossref.lua",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1770"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1766
<div type='discussions-op-text'>
<sup>Originally posted by **ialbert** August 9, 2022</sup>
The `include` tag seems to work only when preceded by whitespace. Example code:
```
Including on a new line works:
{{< include _date.md >}}
this also works:
{{< include _date.md >}}
This does not work: {{< include _date.md >}}
```
the rendered HTML output is:
```
Including on a new line works:
May 26, 2022
this also works:
May 26, 2022
This does not work:
```
is that by design? Thanks.</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-09T19:05:36Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1767,
"state": "open",
"title": "typescript shortcodes need to be in a line by themselves",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1767"
} |
I am using Mac OS Monterey Version 12.5, the latest versions of R (4.2.1), R Studio (2022/07, 1-554), and Quarto (1.0.38), and the `rmarkdown` package (2.14). When attempting to render Quarto (the given `hello.qmd` file), I see the following error:
```
Error in assignInNamespace("htmlPreserve", htmlPreserve, ns = "htmltools") :
could not find function "assignInNamespace"
Calls: .main -> source -> withVisible -> eval -> eval
Execution halted
Error in packageVersion("rmarkdown") :
could not find function "packageVersion"
Calls: cat -> paste0
Execution halted
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
What I have done so far to try to address this issue:
1) Tried to manually set the PATH to the R library(s): https://community.rstudio.com/t/adding-to-the-path-variable/12066
```
old_path <- Sys.getenv("PATH")
Sys.setenv(PATH = paste(old_path, "/Library/Frameworks/R.framework/Resources/library", sep = ":"))
```
2) Tried to override QUARTO_R to (what I believe) is the directory R is in (consulting this [issue](https://community.rstudio.com/t/render-with-quarto-error/134403)).
`Sys.setenv('QUARTO_R' = '/Library/Frameworks/R.framework/Resources')`
FYI, R is working otherwise fine. I am able to use it as normal, so R Studio itself can clearly recognize that its there.
Render is working just fine on my work desktop, which is running an older version of R (4.1.1), but which is otherwise the same (updated OS, RStudio, and Quarto). The only thing I can think of is that on my laptop, there is something problematic going on with administrator privileges. However, I am not sure how to tinker in Terminal to identify the error and set appropriate paths.
Any assistance is greatly appreciated! | {
"assignee": null,
"comments": 4,
"created_at": "2022-08-09T17:22:38Z",
"creator": "EOneita",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1765,
"state": "closed",
"title": "unable to find R installation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1765"
} |
### Bug description
I can't reproduce an example in the Quarto [documentation](https://quarto.org/docs/interactive/layout.html). The example shows how to change the layout of input filters so that the filters are next to each other. When I try to reproduce this, the inputs are below each other. I am on Windows and am running the RStudio version 2022.07.1 Build 554
````md
---
title: Issue with multiple columns in input panel
format:
html:
self-contained: true
code-fold: true
---
```{ojs}
//| panel: input
//| layout-ncol: 3
//| https://quarto.org/docs/interactive/layout.html
viewof color1 = Inputs.checkbox(["red", "green", "blue"], {label: "color1"})
viewof color2 = Inputs.radio(["red", "green", "blue"], {label: "color2"})
viewof rng = Inputs.range(
[1,10],{
value: 3,
step: 1
})
```
````
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.38
Path: C:\Users\wn00198624\AppData\Local\Programs\Quarto\bin\
CodePage: 1250
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[>] Checking R installation...........OK
Version: 4.2.0
Path: C:/Users/wn00198624/AppData/Local/Programs/R/R-4.2.0
LibPaths:
- C:/Users/wn00198624/AppData/Local/Programs/R/R-4.2.0/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```md
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 12,
"created_at": "2022-08-09T15:59:18Z",
"creator": "novotny1akub",
"is_pull_request": false,
"labels": [
"bug",
"windows"
],
"locked": false,
"milestone": null,
"number": 1764,
"state": "closed",
"title": "Can't reproduce Quarto documentation: Component Layout: Input Panel",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1764"
} |
## Problem
Compiling .qmd docs from Windows PowerShell works fine. But while trying to compile from Rstudio it fails.
## Reprex
The test file I'm using comes from the official quarto website: https://quarto.org/docs/get-started/hello/rstudio/_hello.qmd
## Tried attempts
### Powershell
Running `quarto render hello.qmd` within PowerShell works perfectly.
### Rstudio
#### Render Button
If I open the `hello.qmd` file in Rstudio en press the Render button I got the following error:
```
Message d'avis :
Dans system(paste0("quarto render \"", input, "\" ", "--to default")) :
'CreateProcess' a Γ©chouΓ© au lancement de 'C:\Users\TGOOSS~1\AppData\Local\Programs\Quarto\bin\quarto.cmd render "C:/Users/tgoossens/Desktop/test_rmarkdown/test.qmd" --to default'
```
#### R console
If I call `quarto::quarto_render(hello.qmd)` from the R console I got the following error:
```
Error in `process_initialize(self, private, command, args, stdin, stdout, β¦`:
! Native call to `processx_exec` failed
Caused by error in `chain_call(c_processx_exec, command, c(command, args), pty, pty_options, β¦`:
! create process 'C:\Users\TGOOSS~1\AppData\Local\Programs\Quarto\bin\quarto.cmd' (system error 2, The system cannot find the file specified.
) @win/processx.c:1040 (processx_exec)
Type .Last.error to see the more details.
```
Result from `quarto::quarto_path()` :
`[1] "C:\\Users\\TGOOSS~1\\AppData\\Local\\Programs\\Quarto\\bin\\quarto.cmd"`
Result from `quarto::quarto_version()`:
```
Error in system2(quarto_bin, "--version", stdout = TRUE) :
'CreateProcess' failed to run 'C:\Users\TGOOSS~1\AppData\Local\Programs\Quarto\bin\quarto.cmd --version'
```
## Session info :
```
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=French_Belgium.utf8 LC_CTYPE=French_Belgium.utf8 LC_MONETARY=French_Belgium.utf8
[4] LC_NUMERIC=C LC_TIME=French_Belgium.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 ps_1.7.1 digest_0.6.29 later_1.3.0 R6_2.5.1 jsonlite_1.8.0
[7] evaluate_0.15 rlang_1.0.4 cli_3.3.0 rstudioapi_0.13 rmarkdown_2.14 tools_4.2.1
[13] glue_1.6.2 xfun_0.31 yaml_2.3.5 fastmap_1.1.0 compiler_4.2.1 processx_3.7.0
[19] htmltools_0.5.3 knitr_1.39 quarto_1.2
```
## Similar issues/threads :
* https://community.rstudio.com/t/failed-to-run-c-pdflatex-exe/49079/4
* https://github.com/rstudio/tinytex/issues/208
* https://github.com/rstudio/rstudio/issues/5681
* https://community.rstudio.com/t/error-generating-pdf-in-r-markdown/60003
## Remark
The problem was privately discussed with @cderv
=========
Thanks or your help
| {
"assignee": "cderv",
"comments": 11,
"created_at": "2022-08-09T14:19:59Z",
"creator": "pokyah",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 1760,
"state": "closed",
"title": "Quarto-cli called from Rstudio throws 'CreateProcess' failed to run",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1760"
} |
### Bug description
I would like to suggest en #enhancement that I believe would be beneficial for the Users.
The problem is that when author cross references to different part of the document (i.e. equation from different chapter) user is moved back and forth. How about in html format one could hover over the reference and would see the rendered equation (or a small version of the figure)? That would work like a footnote that is presented when hovered over.
I can see that there could be some issues when author is referencing to a range of equations (Equation 1.1 - 1.3).
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-09T12:55:06Z",
"creator": "Belyor",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1757,
"state": "open",
"title": "Hover over eq reference",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1757"
} |
### Bug description
System: Windows10
`_quarto.yml`:
```
project:
type: book
output-dir: docs
book:
title: "My Title"
author: "My Author"
chapters:
- index.qmd
format:
html:
theme: cosmo
code-link: true
include-before-body:
\usepackage{mathtools, simpler-wick}
toc: true
toc-title: Spis sekcji
toc-depth: 2
html-math-method: katex
number-sections: true
number-depth: 1
anchor-sections: true
smooth-scroll: true
```
which contains the [CTAN](https://ctan.org/pkg/simpler-wick) _simpler-wick_ package. According to [documentation](https://jpellis.me/projects/simpler-wick/simpler-wick/simpler-wick.pdf) ine should put `*.sty` file in project root directory (it works when tested on [overleaf.com](https://www.overleaf.com). However, when one `quarto render`'s `index.qmd` file with the codeblock of:
``` latex
$$
\wick{\c\phi A \c\phi}
$$
```
that is expected to produce:
it renders this:
### `quarto check` Output
> quarto check
```
[>] Checking Quarto installation......OK
Version: 1.0.38
Path: C:\Program Files\Quarto\bin\
CodePage: 1250
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.8.13 (Conda)
Path: C:/Users/andrz/AppData/Roaming/jupyterlab-desktop/jlab_server/python.exe
Jupyter: 4.9.2
Kernels: python3
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.1.0
Path: C:/PROGRA~1/R/R-41~1.0
LibPaths:
- C:/Users/andrz/OneDrive/Dokumenty/R/win-library/4.1
- C:/Program Files/R/R-4.1.0/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
> quarto tools check
```
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 7,
"created_at": "2022-08-09T11:08:47Z",
"creator": "Belyor",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1754,
"state": "closed",
"title": "Wick's contractions ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1754"
} |
I seem to have a slight issue using a quarto template I have created. I followed the instructions [here](https://quarto.org/docs/extensions/formats.html), but when I pull the template from the GitHub repo I have made, using
```
quarto use template giabaio/my-repo
```
quarto creates a `giabaio` folder under `_extension`. So the resulting files are
```
new_folder
- new_folder.qmd
- _extensions
- giabaio
- all the stuff that should be under _extension
```
This has repercussions to my workflow, because the `template.qmd` file looks for stuff under `_extensions/name_of_the_template`, which is actually now stored under `_extensions/giabaio/name_of_the_template`.
Am I making some silly mistake? Or do I simply need to remove the `giabaio` folder and place everything else under `_extensions` manually?
Thanks!
Gianluca | {
"assignee": null,
"comments": 5,
"created_at": "2022-08-09T10:54:58Z",
"creator": "giabaio",
"is_pull_request": false,
"labels": [
"verify-fixed"
],
"locked": false,
"milestone": "v1.1",
"number": 1753,
"state": "closed",
"title": "Issue with using quarto template ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1753"
} |
**Background**
The [listings](https://quarto.org/docs/websites/website-listings.html) feature allows one to automatically populate the contents of a page. I expect it was intended for use only in websites, for example an overview of blogposts.
**My Modification**
I used the meta-data of chapters (`title`, `meta-description`) and a listing page to create an informative TOC. So rather than only showing chapter numbers and titles - readers now also see the `meta-description` as part of a table (without filter, sort etc).
**Feature Request**
The educational book we are creating should have both a HTML and a PDF version. Unfortunately, the `listing` page remains empty in the PDF output. I believe the `table` type should be suited for inclusion in a PDF - which is why I want to request it as a feature. | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-09T10:17:32Z",
"creator": "SHogenboom",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1752,
"state": "open",
"title": "Feature Request: (Table) Listings for PDF",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1752"
} |
The penguins example in the [OJS](https://quarto.org/docs/interactive/ojs/) and [standalone example](https://quarto.org/docs/interactive/ojs/examples/penguins.html) uses a version of the `palmerpenguins` dataset that varies from the R package itself, namely, removing the units from the col names.
```
names(palmerpenguins::penguins)
[1] "species" "island" "bill_length_mm" "bill_depth_mm"
[5] "flipper_length_mm" "body_mass_g" "sex" "year"
```
```
names("palmer-penguins.csv")
[1] "species" "island" "bill_length" "bill_depth" "flipper_length"
[6] "body_mass" "sex"
```
This makes sense for the example but is a bit surprising if someone were to try:
```
ojs_define(data = palmerpenguins::penguins)
```
As the colnames mismatch will silently fail at the OJS level - the plots will not be returned and the only errors are seen in the console of the browser itself at JavaScript level. I would suggest either being very clear and providing a direct URL to the used .csv (rather than having to go find it on GitHub) and/or clarifying the changed col names.
Tag @cscheid from our discussion. | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-08T20:23:31Z",
"creator": "jthomasmock",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 1878,
"state": "closed",
"title": "`penguins` example for OJS uses a modified version of the palmer-penguins.csv",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1878"
} |
How do I set position of slide numbers or logo? Seems like when you remove the logo from the yaml header, the slide numbering goes to bottom right from top right. How do I put it at the top right without using the logo? | {
"assignee": "cderv",
"comments": 3,
"created_at": "2022-08-08T19:33:25Z",
"creator": "ghost",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 1879,
"state": "open",
"title": "Slide number, logo positioning",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1879"
} |
### Bug description
After installing `quarto-1.0.38-win.msi` (Windows 10), I get an error when I try to run quarto cli:
```
'"C:\Users\{username}\AppData\Local\Programs\Quarto\bin\\tools\deno"' is not recognized as an internal or external command,
operable program or batch file.
```
Contents of the folder where it's looking:
Note: this was during an attempt to upgrade from a previous version from June.
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-08T15:45:37Z",
"creator": "lukesdm",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1739,
"state": "closed",
"title": "'\"C:\\Users\\{username}\\AppData\\Local\\Programs\\Quarto\\bin\\\\tools\\deno\"' is not recognized as an internal or external command, operable program or batch file.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1739"
} |
### Bug description
The space between the entity type ("Figure", "Table",...) and its number in the entity label should be a non breaking space instead of a plain space, like in the cross reference link.
---
format: html
---
See @fig-test
```{r}
#| label: fig-test
#| fig-cap: "Test"
plot(1)
```
producing :
...
<p>See <a href="[#fig-test](#fig-test)">Figure 1</a></p>
...
<figcaption class="figure-caption">Figure 1: Test</figcaption>
...
The figcaption text should have a ` ` like in the anchor :
<figcaption class="figure-caption">Figure 1: Test</figcaption>
* it will be similar between the crossref text and the label
* it's a common typographic convention
Thanks
RStudio 2022.07.1 Build 554
windows 10
### `quarto check` Output
```bash
[>] Checking Quarto installation......OK
Version: 1.0.36
Path: C:\Program Files\RStudio\bin\quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....(None)
Unable to locate an installed version of Python 3.
Install Python 3 from https://www.python.org/downloads/
[>] Checking R installation...........OK
Version: 4.1.1
Path: C:/PROGRA~1/R/R-41~1.1
LibPaths:
- C:/Users/xxx/Documents/R/win-library/4.1
- C:/Program Files/R/R-4.1.1/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-08T15:33:03Z",
"creator": "dicorynia",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1738,
"state": "closed",
"title": "Add non breaking space in caption label",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1738"
} |
Like this:
https://github.com/quarto-dev/quarto-cli/commit/c8b34b2166efb328434fe8655d75f804872f2a40 | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-08-08T13:51:23Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1732,
"state": "closed",
"title": "Terminal Progress Bar should be compact when running in CI",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1732"
} |
{
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-08T11:06:39Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1731,
"state": "closed",
"title": "publish: auth error during slugAvailable not handled",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1731"
} |
|
### Bug description
Consider the following minimal working example:
`_quarto.yml`:
```
project:
type: book
book:
title: "Minimal Working Example"
author: "Raniere Silva"
date: "08/08/2022"
chapters:
- index.qmd
always_allow_html: true
format:
html:
theme: cosmo
docx:
lang: en
```
`index.qmd`:
``````
# Preface {.unnumbered}
This is a Quarto book.
```{r}
#| echo: true
#| warning: false
#| error: false
#| output: false
library(ggplot2)
library(plotly)
```
```{r}
#| echo: true
#| warning: false
#| error: false
#| output: false
p <- iris |>
ggplot(aes(
x = Petal.Length,
y = Petal.Width
)) +
geom_point()
```
::: {#fig-iris}
::: {.content-visible unless-format="html"}
```{r}
#| echo: false
#| warning: false
#| error: false
#| output: true
p
```
:::
::: {.content-visible when-format="html"}
```{r}
#| echo: true
#| warning: false
#| error: false
#| output: true
p |>
ggplotly() |>
layout(dragmode = "pan")
```
:::
Chart using Edgar Anderson's Iris Data.
:::
``````
When I render it to a MS Word, I get
```
processing file: index.qmd
|........ | 11%
ordinary text without R code
|................ | 22%
label: unnamed-chunk-1 (with options)
List of 5
$ echo : logi TRUE
$ warning: logi FALSE
$ error : logi FALSE
$ output : logi FALSE
$ message: logi FALSE
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
|....................... | 33%
ordinary text without R code
|............................... | 44%
label: unnamed-chunk-2 (with options)
List of 5
$ echo : logi TRUE
$ warning: logi FALSE
$ error : logi FALSE
$ output : logi FALSE
$ message: logi FALSE
|....................................... | 56%
ordinary text without R code
|............................................... | 67%
label: unnamed-chunk-3 (with options)
List of 5
$ echo : logi FALSE
$ warning: logi FALSE
$ error : logi FALSE
$ output : logi TRUE
$ message: logi FALSE
|...................................................... | 78%
ordinary text without R code
|.............................................................. | 89%
label: unnamed-chunk-4 (with options)
List of 5
$ echo : logi TRUE
$ warning: logi FALSE
$ error : logi FALSE
$ output : logi TRUE
$ message: logi FALSE
|......................................................................| 100%
ordinary text without R code
output file: index.knit.md
Error: Functions that produce HTML output found in document targeting docx output.
Please change the output type of this document to HTML. Alternatively, you can allow
HTML output in non-HTML formats by adding this option to the YAML front-matter of
your rmarkdown file:
always_allow_html: true
Note however that the HTML output will not be visible in non-HTML formats.
Execution halted
```
The error message is clear. Add `always_allow_html: true` to the rmarkdown file solve the problem. Would be possible to propagate the `always_allow_html: true` from `_quarto.yml` to the rmarkdown file?
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.37
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/
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-08-08T04:09:06Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1729,
"state": "closed",
"title": "Propagate 'always_allow_html: true' from _quarto.yml to the .Rmd",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1729"
} |
### Bug description
Hi! Why the following code does not return the output expected ? Is there a way to set the whole document to return the same print from R code?
``````md
---
title: "Accessing variable from code chunk"
format:
pdf:
toc: false
number-sections: false
---
# Behavior
```{r}
x <- 10011
```
Printing the result: `r x`
# Behavior expected
```{r}
y <- 10011
```
Printing the result: 10011
``````
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-08-07T22:59:37Z",
"creator": "Gabrielforest",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1725,
"state": "closed",
"title": "Accessing variable from code chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1725"
} |
### Bug description
I tried to switch to the new quarto-publish GitHub Actions workflow for my blog and was hit with this
```
ERROR: No previous publishes available to re-publish (previous publish required with --no-prompt)
```
https://github.com/DavisVaughan/blog/runs/7715534347?check_suite_focus=true
I realized after reading more of the documentation that I needed to run `quarto publish netlify` once locally to create the `_publish.yml` locally (I ended up modifying the once it created with my pre-existing site ID and URL, but it was a useful skeleton).
Could this error message suggest: `` "Do you need to run `quarto publish netlify` locally?" ``
Error comes from here https://github.com/quarto-dev/quarto-cli/blob/3c6fa936a0c9a6ae36f127daf4c3b05c83a99f60/src/command/publish/deployment.ts#L117
Quarto 1.0.35
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-07T20:39:58Z",
"creator": "DavisVaughan",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1724,
"state": "closed",
"title": "Improve error message when you need to run `quarto publish netlify` once locally",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1724"
} |
### Bug description
Hi! This was interesting issue to pin down: rendering plain .qmd with special characters (the letter **Ε‘** to be precise) to .html works on my machine but fails to render them when there's an r code chunk inside the file. My .qmd file contains special characters and the file was saved as UTF-8.
# Reprex
To reproduce, render the following content in a .qmd file to .html (GitHub doesn't allow attaching .qmd files?):
```
---
title: "Funky .qmd file"
---
The following are special characters:
Δ
ΔΔΔΔ―Ε‘Ε³Ε«
```{r}
plot(pressure)
```
```
# Output
The rendered .html file body contains the following text:
```
<html>
<body>
<!--StartFragment-->
<p>The following are special characters:</p>
--
Β | <p>Δ
ΔΔΔΔ―</p>
<!--EndFragment-->
</body>
</html>
```
And the console throws the following warning:
```
Warning messages:
1: In readLines(con, warn = FALSE) :
invalid input found on input connection 'index.qmd'
2: In xfun::read_utf8(input) :
The file index.qmd is not encoded in UTF-8. These lines contain invalid UTF-8 characters: 8
3: In readLines(con, warn = FALSE) :
invalid input found on input connection 'index.knit.md'
4: In readLines(con, warn = FALSE) :
invalid input found on input connection './index.knit.md'
5: In readLines(con, warn = FALSE) :
invalid input found on input connection 'index.qmd'
```
This seems to be an issue with `knitr` having trouble with special characters but I've tried rendering the same content using the `knitr` package from .Rmd to .md via knitr, and from .md to .html via quarto...and it worked? I think the problem stems from differences in what knitr engine Quarto uses and the `knitr` package itself but I'm not sure how to troubleshoot further. Help appreciated!
# Session Info
```
R version 4.1.3 (2022-03-10)
RStudio v2022,07.1
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=Lithuanian_Lithuania.1257 LC_CTYPE=Lithuanian_Lithuania.1257
[3] LC_MONETARY=Lithuanian_Lithuania.1257 LC_NUMERIC=C
[5] LC_TIME=Lithuanian_Lithuania.1257
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 ps_1.7.1 digest_0.6.29 later_1.3.0 R6_2.5.1 jsonlite_1.8.0
[7] magrittr_2.0.2 evaluate_0.15 highr_0.9 stringi_1.7.6 rlang_1.0.2 cli_3.3.0
[13] renv_0.15.5 rstudioapi_0.13 rmarkdown_2.14 tools_4.1.3 stringr_1.4.0 xfun_0.30
[19] yaml_2.3.5 fastmap_1.1.0 compiler_4.1.3 processx_3.7.0 htmltools_0.5.2 knitr_1.38
[25] quarto_1.2
```
### `quarto check` Output
```
[>] Checking Quarto installation......OK
Version: 1.0.37
Path: C:\Users\Paulius\AppData\Local\Programs\Quarto\bin\
CodePage: 1257
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.8.3
Path: C:/Users/Paulius/AppData/Local/Programs/Python/Python38-32/python.exe
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with py -m pip install jupyter
[>] Checking R installation...........OK
Version: 4.1.3
Path: C:/PROGRA~1/R/R-41~1.3
LibPaths:
- C:/Users/Paulius/Documents/R/win-library/4.1
- C:/Program Files/R/R-4.1.3/library
rmarkdown: 2.13
```
[>] Checking Knitr engine render......OK
### `quarto tools check` Output
```
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-08-07T20:22:51Z",
"creator": "Alaburda",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1723,
"state": "closed",
"title": ".qmd stops rendering at special characters if there is an r code chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1723"
} |
{
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-07T15:18:19Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1722,
"state": "closed",
"title": "add code-block filename as a built-in feature",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1722"
} |
|
{
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-07T15:17:47Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1721,
"state": "closed",
"title": "add sticky tabs as a built in feature",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1721"
} |
|
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1690
<div type='discussions-op-text'>
<sup>Originally posted by **schochastics** August 4, 2022</sup>
Hi there,
What would be the best way (if there is any) to include a button on a rendered ipynb which opens the notebook on google colab (see example at the bottom)?
I could of course do it manually, but I have a lot of notebooks to render for a website which I pull from github.
Is this maybe possible with ipynb filters? If so, any pointer would be greatly appreciated since I am an utter python noob.
/Edit:
After some more research I found that [jupyterbook](https://jupyterbook.org/en/stable/intro.html) has this feature.
</div> | {
"assignee": "jjallaire",
"comments": 3,
"created_at": "2022-08-07T13:40:58Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1718,
"state": "open",
"title": "Button to open rendered ipynb in google colab",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1718"
} |
### Bug description
_No response_
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [ ] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-07T13:18:33Z",
"creator": "jjallaire",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1717,
"state": "closed",
"title": "don't use spinner in terminal when running on ci",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1717"
} |
### Bug description
Consider the following minimal working example:
`_quarto.yml`:
```
project:
type: book
book:
title: "Minimal Working Example"
doi: "reserved/identifier"
author: "Raniere Silva"
date: "07/08/2022"
chapters:
- index.qmd
bibliography: references.bib
format:
html:
theme: cosmo
```
`index.qmd`:
```
# Preface {.unnumbered}
This is a Quarto book.
To learn more about Quarto books visit <https://quarto.org/docs/books>.
```
I expected to see the DOI in next to the title like in the "normal" document but the DOI is not visible.
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.2
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /opt/conda/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-08-07T08:57:26Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1714,
"state": "closed",
"title": "Show DOI for book",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1714"
} |
Not so much an issue for my personal use, but my organization has disabled `.cmd` files except with admin permissions.
PowerShell, on the other hand, is allowed and would facilitate adoption much more readily | {
"assignee": null,
"comments": 3,
"created_at": "2022-08-06T18:48:13Z",
"creator": "cooknl",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 1880,
"state": "closed",
"title": "Why .cmd? Please port to PowerShell",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1880"
} |
There is a problem on: [quarto-web / docs / presentations / revealjs / index.qmd
](https://quarto.org/docs/presentations/revealjs/#line-highlighting)
The code block below:
>You can use this same option within an executable code cell by using the code-line-numbers cell options:
shows/says `#echo: fenced`. So when the code is rendered the lines with the hash pipes are shown/counted:
```{.python}
#| echo: fenced
#| code-line-numbers: "|6|9"
import numpy as np
import matplotlib.pyplot as plt
r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(subplot_kw={'projection': 'polar'})
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()
```
That is not what is shown in the imbedded content below the code block. That code (I think) comes from here:
<https://github.com/quarto-dev/quarto-web/blob/main/docs/presentations/revealjs/examples/line-highlighting-4.qmd>
*line-highlighting-4.qmd* has `#| echo: true` instead of `#|echo:fenced`. So the line numbers do not match. Instead of showing what is on the web page (https://quarto.org/docs/presentations/revealjs/):
... the code running `echo:fenced` highlights a blank line.
<img width="1839" alt="image" src="https://user-images.githubusercontent.com/18148282/183258863-8d9c2d30-5999-447e-8a6a-16d902817a5d.png">
I am thinking both code chunks should use `echo:true` and `echo:fenced` should be explained later.
Also it is very confusing to show code that does not execute in a paragraph about executable code. Notice the code block shows `.python` instead of `python`. So.... I think the shown code should be:
````
```{python}
#| echo: echo
````
| {
"assignee": "cderv",
"comments": 1,
"created_at": "2022-08-06T17:10:15Z",
"creator": "RaymondBalise",
"is_pull_request": false,
"labels": [
"bug",
"documentation"
],
"locked": false,
"milestone": "v1.3",
"number": 1881,
"state": "closed",
"title": "Code and output do not match in the final example in https://quarto.org/docs/presentations/revealjs/#line-highlighting",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1881"
} |
### Bug description
Installing quarto preview to test out a possible bugfix for issue #1320
It seems like a unix path, but I'm on Windows.
Git blame suggests https://github.com/quarto-dev/quarto-cli/commit/53e730e267e418a30c69a779fb735235d74740fd#diff-5918f8cb78f1ee5f520dadb760486aa0776451a52675a0f239c1829ff498f8c1 is when the issue was introduced.
### `quarto check` Output
```bash
C:\Users\burge\GitHub\quarto-web>quarto check
[>] Checking Quarto installation......OK
Version: 1.1.48
Path: C:\Users\burge\AppData\Local\Programs\Quarto\bin\
CodePage: 65001
[>] Checking basic markdown render....OK
ERROR: NotFound: The system cannot find the path specified. (os error 3), open '/tmp/file1'
```
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-06T16:47:14Z",
"creator": "burgerga",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1713,
"state": "closed",
"title": "ERROR: NotFound: The system cannot find the path specified. (os error 3), open '/tmp/file1'",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1713"
} |
Quarto version: I tried a few version. Started with 1.0.37 then I updated to the latest dev version (says 99.9.9) using this
```
git clone https://github.com/quarto-dev/quarto-cli
cd quarto-cli
./configure-macos.sh
```
Then went back to v1.0.38 by re-installing.
RStudio: 2022.02.2
OS: Mac Big Sur 11.6.2
This is specific to a Quarto book project.
If have 2 h1 headers in a chapter qmd, the first appears in TOC and the others appear with the right sequential chapter numbers but don't appear in the TOC and later chapters don't "know" about the new chapters.
Example `_quarto.yml`
```
project:
type: book
book:
title: "test"
chapters:
- index.qmd
- chap1and2.qmd
- chap3.qmd
format:
html:
theme: cosmo
```
`chap1and2.qmd`
```
# Chapter 1
This is chapter 1
# Chapter 2
This is chapter 2
```
This is the output. Notice the TOC.
<img width="662" alt="image" src="https://user-images.githubusercontent.com/2545978/183253088-e90f396a-43fc-4253-b199-50c865c61326.png">
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.12
Path: /opt/homebrew/opt/[email protected]/bin/python3.9
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.1.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/eli.holmes/Library/R/x86_64/4.1/library
- /Library/Frameworks/R.framework/Versions/4.1/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
### Use case, why is this needed?
In report writing situation, you often don't know how many chapters (appendices) you will need. You are using `knit_expand()` with an child.Rmd that is creating all your chapters (appendices) based on the data (which vary). That `knit_expand()` is a for loop (or map function) and is creating the markdown dynamically. This works fine in Quarto...except that it doesn't recognize the later h1 levels as proper chapters.
### Checklist
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [x] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [x] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 6,
"created_at": "2022-08-06T14:36:36Z",
"creator": "eeholmes",
"is_pull_request": false,
"labels": [
"enhancement",
"books"
],
"locked": false,
"milestone": "v1.4",
"number": 1712,
"state": "open",
"title": "Quarto book: multiple chapters in one qmd chapter",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1712"
} |
### Bug description
`fig-cap` is not showing at the right place when `fig-subcap` option is set in OJS.
A qmd fie containing a minimal example is here:
[ojs-cap.zip](https://github.com/quarto-dev/quarto-cli/files/9275162/ojs-cap.zip)
RStudio: 2022.11.0-daily+82
OS: Linux 5.15.0-43-generic Ubuntu 22.04
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 1.1.46
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.4
Path: /usr/bin/python3
Jupyter: 4.11.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.1.2
Path: /usr/lib/R
LibPaths:
- /home/sushovan/R/x86_64-pc-linux-gnu-library/4.1
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
### `quarto tools check` Output
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-08-06T14:02:49Z",
"creator": "sushovan4",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1711,
"state": "closed",
"title": "Fig Sub-captions Not Functional in OJS",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1711"
} |
### Bug description
Tables with markdown or html have to have `escape = FALSE` to not show the markdown or html verbatim when displaying in a table with kable().
- If you you display the table with `knitr::kable()`, both types of links display correctly as links
- If you use `kableExtra::kable()`, the markdown version just shows the markdown verbatim
- However, if you `unclass()` the result of the kableExtra version, it does display markdown links correctly
- The reprex below shows these problems in a .qmd file, but not if knit in an .Rmd file
Reprex of the problem:
````
---
title: "kableExtra Escape Reprex"
format: html
---
Create table with markdown and html links:
```{r}
tbl <- data.frame(
markdown = "[github](https://github.com)",
html = "<a href='https://github.com'>github</a>"
)
```
Both work with knitr::kable()
```{r, results='asis'}
knitr::kable(tbl, escape = FALSE)
```
The markdown version doesn't work with kableExtra::kable()
```{r, results='asis'}
kableExtra::kable(tbl, escape = FALSE)
```
But if you unclass() and cat() the result, it does work:
```{r, results='asis'}
kableExtra::kable(tbl, escape = FALSE) |>
unclass() |> cat()
```
````
<img width="828" alt="kableExtra-quarto" src="https://user-images.githubusercontent.com/14863295/183250174-150280f1-7c43-4d60-887f-5bd8ac6c338c.png">
### `quarto check` Output
FYI: for RStudio users who aren't familiar with the command line, you might want to instruct them to paste the output of `quarto::quarto_path() |> paste("check") |> system()`.
```bash
[β] Checking Quarto installation......OK
Version: 1.0.36
Path: /Applications/RStudio.app/Contents/MacOS/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.7.3
Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
I'm running RStudio 2022.07.1 Build 554
"Spotted Wakerobin" Release (7872775e, 2022-07-22) for macOS
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) QtWebEngine/5.12.10 Chrome/69.0.3497.128 Safari/537.36
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-06T12:56:33Z",
"creator": "debruine",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1710,
"state": "open",
"title": "kableExtra tables not processing markdown",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1710"
} |
Hey everyone,
Has there been discussion about adding some sort of SI unit formatting to quartio, similar to what `siunitx` allows for LaTeX?
This sort of thing is quite helpful when working with derived SI units, or prefixes that aren't found on latin keyboards. `siunitx` ([documentation here](https://texdoc.org/serve/siunitx/0)) handles this in LaTeX, and it would be nice to somehow bring this functionality over.
`siunitx` ensures that the units are formatted consistently, with a required nonbreaking space between number and unit. It also has some nice features for things like formatting angles, lists, and ranges. As examples, `\qty{30}{\uA}` is rendered as "30 ¡A", `\qty{70}{\Mohm\per\um}` as "70 M⦠¡m^-1" (with the correct exponent of course), `\ang{180}` as "180°" , or `\qtyrange{0.15}{30}{\MHz}` as "0.15 MHz to 30 MHz. (There are a lot more examples in the PDF documentation linked above).
Something like this would be a very nice fit for Quarto's use in scientific documentation. | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-06T05:55:23Z",
"creator": "tgross35",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1708,
"state": "open",
"title": "Suggestion: Add builtin support for SI unit formatting",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1708"
} |
### Bug description
Consider the following minimal working example:
`_quarto.yml`:
```
project:
type: book
book:
title: "Minimal Working Example"
author: "Raniere"
date: "06/08/2022"
chapters:
- index.qmd
format:
html:
theme: cosmo
```
`index.qmd`:
```
# Preface {.unnumbered}
Some text [@fig-first; @fig-second] more text.
{#fig-first}
{#fig-second}
```
After render, I got
> Some text Figure 1, Figure 2 more text.
when I expected to get
> Some text Figure 1--2 more text.
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.2
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /opt/conda/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
### `quarto tools check` Output
```
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-06T00:18:32Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 1707,
"state": "open",
"title": "Use dash (-) with group cross references",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1707"
} |
### Bug description
Consider the following minimal working example:
`_quarto.yml`:
```
project:
type: book
book:
title: "Minimal Working Example"
author: "Raniere"
date: "06/08/2022"
chapters:
- index.qmd
format:
html:
theme: cosmo
```
`index.qmd`:
```
# Preface {.unnumbered}
Some text [@fig-first; @fig-second] more text.
{#fig-first}
{#fig-second}
```
After render, I got
> Some text Figure 1, Figure 2 more text.
when I expected to get
> Some text Figure 1 and Figure 2 more text.
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.2
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /opt/conda/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-06T00:16:39Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 1706,
"state": "open",
"title": "Use \"and\" before last reference in group cross references",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1706"
} |
### Bug description
Consider the following minimal working example:
`_quarto.yml`:
```
project:
type: book
book:
title: "Minimal Working Example"
author: "Raniere"
date: "06/08/2022"
chapters:
- index.qmd
appendices:
- supplement.qmd
format:
html:
theme: cosmo
```
`index.qmd`:
```
# Preface {.unnumbered}
Some text @sec-foo.
```
`supplement.qmd`:
```
# Foo {#sec-foo}
Some text.
```
When render, I got
> Some text Chapter A.
when I expect to get
> Some text Appendix A.
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.2
Path: /usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.1.3
Path: /opt/conda/lib/R
LibPaths:
- /opt/conda/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-06T00:09:26Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1705,
"state": "closed",
"title": "When cross-referencing Appendix, use \"Appendix X\" instead of \"Chapter X\". ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1705"
} |
### Bug description
When setting the `site` parameter in `website.twitter-card` in `_quarto.yml`, the @username isn't stripped out and causes a pandoc warning when rendering the site:
``` yaml
website:
twitter-card:
creator: "@creatorname"
site: "@sitename"
```
```
[WARNING] Citeproc: citation sitename not found
```
This was fixed in https://github.com/quarto-dev/quarto-cli/commit/46583c653c2f5cdb8df3089f2ff1ffe9174c918b for the `twitter-card.creator` parameter, but not for `twitter-card.site`. The warning does not appear when omitting `site` in the YAML file, as expected.
I'm using macOS 12.4, R 4.2.1, Quarto 1.0.38, and RStudio 2022.07.1 Build 554
### `quarto check` Output
``` text
[β] Checking Quarto installation......OK
Version: 1.0.38
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.13
Path: /opt/homebrew/opt/[email protected]/bin/python3.9
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
``` text
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-08-05T19:54:14Z",
"creator": "andrewheiss",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1702,
"state": "closed",
"title": "Citeproc warning when using twitter-card.site",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1702"
} |
I have a test extension ([tarleb/test-extension](https://github.com/tarleb/test-extension)) that tries to keep a file outside of the `_extensions` folder. I'd like to use a symlink to make that file part of the extension. However, `quarto install extension tarleb/test-extension` copies the symlink, which will usually point to a nonexisting file after the installation.
Here's the file structure of the source repository:
```
.
βββ _extensions
βΒ Β βββ test-extension
βΒ Β βββ _extension.yml
βΒ Β βββ test-extension.lua -> ../../test-extension.lua
βββ test-extension.lua
```
It would be convenient if the symlinks below `_extensions` could be replaced with the files/dirs that they point to, at least if those link targets are outside of the `test-extension` folder.
Background: I'd like to update the `tarleb/lua-filter-template` and make it easy for users of that template to provide filters as quarto extensions. Symlinking the filter would seem like a simple solution for that. | {
"assignee": null,
"comments": 7,
"created_at": "2022-08-05T18:46:56Z",
"creator": "tarleb",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1700,
"state": "closed",
"title": "Resolve symlinks when installing an extension.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1700"
} |
### Bug description
The `layout-ncol` option for rendering a multi-column layout is not functional inside ojs code chucks. Despite having set the option `layout-ncol: 2`, the produced plots are stacked vertically.
A qmd fie containing a minimal example is here:
[ojs-plots.zip](https://github.com/quarto-dev/quarto-cli/files/9270061/ojs-plots.zip)
RStudio: 2022.11.0-daily+82
OS: Linux 5.15.0-43-generic Ubuntu 22.04
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.4
Path: /usr/bin/python3
Jupyter: 4.11.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.1.2
Path: /usr/lib/R
LibPaths:
- /home/sushovan/R/x86_64-pc-linux-gnu-library/4.1
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
### `quarto tools check` Output
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-05T15:56:47Z",
"creator": "sushovan4",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 1698,
"state": "closed",
"title": "Multi-column layout not supported for OJS",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1698"
} |
I'd like to suggest a first-class glossary in quarto, where you can link terms in the text to definitions (perhaps displayed on hover) and collect defined terms into an optional glossary table or section at the end of a chapter or the end of a book.
See this [twitter thread](https://twitter.com/LisaDeBruine/status/1555543054974599169) for discussion about this with Thomas Mock and the [psyTeachR glossary package](https://psyteachr.github.io/glossary/) for a model of what I'm thinking about, implemented in R.
## Some ideas
It could require defining terms somehow in the text each time, like:
`{{< gls [term](This is my definition.) >}}`
Or there could be a glossary file similar to `_variable.yml` that you can use to link terms to:
`{{< gls [text-term](file-term) >}}`
This letter option might be better, as you often want to link the same term several times, or link different forms (e.g., the definition might be for "argument", but your sentence is "There are several arguments you need to set."). | {
"assignee": "cscheid",
"comments": 8,
"created_at": "2022-08-05T14:38:00Z",
"creator": "debruine",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 1697,
"state": "open",
"title": "Feature request: Glossary",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1697"
} |
First of all, thank you for this amazing tool!
***
One of the best features of Julia are the super easy project-specific environments, which are captured in the file `Project.toml`. These are meant to be independent of IJulia kernels (unlike conda+python).
What is the default behaviour of Quarto when a `.qmd` file is rendered within a project with `Project.toml` file available?
What is the recommended approach to make sure that a file is rendered in a prescribed environment?
Is it to simply include an explicit cell with `Pkg`, eg,
```
```{julia}
##| echo: false
##| output: false
using Pkg; Pkg.activate(".",io=devnull)
```
?
Thank you
| {
"assignee": null,
"comments": 3,
"created_at": "2022-08-05T12:15:34Z",
"creator": "svilupp",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1696,
"state": "closed",
"title": "Question: How are Julia environments handled? How to render with a project-specific environment?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1696"
} |
When index.qmd contains an r code chunk, rendering to epub creates an invalid epub file, that also can't opened as a zip file.
Example to reproduce this problem:
Create a Quarto Book from RStudio. When you specify Knitr as engine then the generated files index.qmd, intro.qmd and summary.qmd contain a simple r chunk. When you specify None as engine then you should add manuallly an R chunk to index.qmd.
Then add "epub: default" to "format:" in _quarto.yml (or replace the existing formats). After rendering the book to this or all formats, an epub file is created. But you can't open the file with an epub reader (Calibre) or with an zip app.
Remove the r chunk from index.qmd and render the book again to get a valid epub.
Used Quarto version: 1.0.37 (Windows 10) | {
"assignee": "jjallaire",
"comments": 2,
"created_at": "2022-08-05T09:36:40Z",
"creator": "bwelman",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1695,
"state": "closed",
"title": "Invalid epub created when index.qmd contains r code chunk",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1695"
} |
Pandoc v2.19 is out: https://github.com/jgm/pandoc/releases/tag/2.19 | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-05T05:37:35Z",
"creator": "benz0li",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1692,
"state": "closed",
"title": "Enhancement: Update pandoc version",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1692"
} |
If the .qmd file is stored in a the "script" subdirectory and the .yml file specifies `output-dir: output` the resulting files will be rendered into a new script directory nested within the output directory.
I thought specifying `execute-dir: project` would avoid this issue, but it does not.
Please see below for a graphical demonstration:
before rendering:
project
|----.gitignore
|----_quarto.yml
|-------project:
|----------title: "some-proj"
|----------output-dir: script
|----README.md
|----some-proj.Rproj
|___script
|---------| some-proj.qmd
|___output
after rendering:
project
|----.gitignore
|----_quarto.yml
|-------project:
|----------title: "some-proj"
|----------output-dir: script
|----README.md
|----some-proj.Rproj
|___script
|---------| some-proj.qmd
|___output
**|-----------|____script
|---------------------| some-proj.html
|---------------------| some-proj_files__**
| {
"assignee": null,
"comments": 3,
"created_at": "2022-08-05T00:20:16Z",
"creator": "Rory-OG",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1691,
"state": "closed",
"title": "output-dir: output stores files in a new script directory while rendering if .qmd file is in a script subdirectory within quarto project",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1691"
} |
### Bug description
I am running quarto via `quarto preview` on the blog containing the jupyter notebooks in environment
```bash
$ cat /etc/os-release
NAME="Ubuntu"
VERSION="21.04 (Hirsute Hippo)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 21.04"
```
The issue is following:
Plotly figures are sometime not rendered properly.
The below is printing the same figures twice. Only the second one is shown
<img width="551" alt="Screen Shot 2022-08-04 at 1 59 04 PM" src="https://user-images.githubusercontent.com/3666080/182951570-bb28d113-a4f9-44b9-92e3-5836ec2f6db7.png">
I am doing this with jupyter notebook
```
#!/usr/bin/env python
# coding: utf-8
---
title: "2022-08-04--test-jupyter"
author: "My Name"
date: "2022-08-04"
categories:
- quarto
- visualization
execute:
echo: true
format:
html:
theme: cyborg
page-layout: full
toc: true
toc-depth: 5
number-sections: true
self-contained: true
smooth-scroll: true
smooth-scroll: true
code-line-numbers: true
#code-fold: true
#code-tools: false
---
# # Toc
# In[2]:
import plotly.express as px
import plotly
# In[3]:
plotly.offline.init_notebook_mode(connected=True)
# In[4]:
import pandas as pd
# In[5]:
import pandas as pd
df = pd.DataFrame({'a': [1, 2,3]})
# In[6]:
df
# ## Sub Toc
# In[7]:
fig = px.scatter(df, x='a')
# <!-- plotly guard -->
#
#
#
#
# <!-- yes -->
# In[10]:
fig
# In[11]:
fig
```
### `quarto check` Output
```bash
myuser@266e6f1bc382:/org/contributors/myuser/scratch/2022-07-22--quarto-website$
myuser@266e6f1bc382:/org/contributors/myuser/scratch/2022-07-22--quarto-website$ quarto check
[β] Checking Quarto installation......OK
Version: 1.1.38
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.5
Path: /usr/bin/python3
Jupyter: 4.11.1
Kernels: python3, ir
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.0.4
Path: /usr/lib/R
LibPaths:
- /home/myuser/R/x86_64-pc-linux-gnu-library/4.0
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.6
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
$ quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-04T21:04:33Z",
"creator": "grepinsight",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1689,
"state": "closed",
"title": "some plotly figures are not rendered (unpredictably)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1689"
} |
### Bug description
## Unexpected Behaviour in Date Processing
This date format:
```
---
date: 04 08 2022
date-format: "Do MMMM YYYY"
lang: en-GB
---
```
correctly produces `4th August 2022` however other entry formats use American date interpretations.
According to the documentation [dates](https://quarto.org/docs/reference/dates.html), this is how it is described, however, it is surprising not to respect the geographic region of the locale `en-GB`
> The [lang](https://pandoc.org/MANUAL.html#language-variables) document option is used to identifies the main language of the document using IETF language tags (following the [BCP 47](https://tools.ietf.org/html/bcp47) standard), such as en or en-GB.
>
> ...as well as the application of other language specific rules to document processing. - [lang-option](https://quarto.org/docs/authoring/language.html#lang-option)
## Expected Behaviour
```
---
title: Test
date: 04/08/2022
date-format: "Do MMMM YYYY"
lang: en-GB
---
```
Results in `4th August 2022` not ~~`8th April 2022`~~
## Comparison to Pandoc native behaviour
Having used Pandoc for a while I thought that this worked, however it appears that I was mistaken and Pandoc doesn't format dates. I maybe wrong.
## Additional Info
OS: Linux/Ubuntu 22.04
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.4
Path: /usr/bin/python3
Jupyter: 4.11.1
Kernels: python3, julia-1.6, julia-1.7
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
### `quarto tools check` Output
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 8,
"created_at": "2022-08-04T20:10:27Z",
"creator": "a2k42",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1688,
"state": "closed",
"title": "Unexpected Behaviour in Locale Date Processing",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1688"
} |
(Something's happening with our version of `require`.)
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1682
<div type='discussions-op-text'>
<sup>Originally posted by **stuvjordan-uroc** August 4, 2022</sup>
I'm wanting to include some Observable charts in a website I'm building with Quarto. I'd like these charts to include nicely-typeset math, and for that purpose I'm wanting to use MathJax's `tex2svg` function in the source code. Relative to other math typesetting solutions one can use in Observable, `tex2svg` is nice because it outputs pure SVG paths...Thus they scale as the svg containing them is resized without any additional code, so the math looks great on every screen size.
I'm running into this **very** weird difference in the result of a call to `require` when that call is made in an Observable Notebook, as opposed to when I make it in an `ojs` cell in a Quarto sourcefile.
First, let's look at what happens when we require `tex2svg` in an Observable Notebook. You can see the results in [this notebook](https://observablehq.com/@stuvjordan/requiring-mathjax-tex2svg). Open up the object in the first cell after the title and notice the full list of methods that the object returned by the call to `require` includes. Notice the list includes the method `.tex2svg`, which is the function I need. Below is a screenshot. You'll see `tex2svg` as the fourth method from the bottom.
OK, great, so we can use `tex2svg` in an Observable notebook!
But what happens when we do the same call to `require` in an `ojs` cell in a `.qmd` file? Here are two cells from my current `.qmd` source:
```{ojs}
//| output: true
MathJax = require('https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-svg.js').catch(
() => window['MathJax']
)
```
```{ojs}
MathJax
```
Here's a screenshot of the output from the second of the above two `ojs` cells when I render/preview the sourcefile:
**Notice that the list of methods does not include `tex2svg`!!!!** As a result, when I do something like
```{ojs}
MathJax.tex2svg(
String.raw`\int_0^1 \exp(x)dx`
);
```
In the quarto sourcefile, the output on render/preview is:
I'm kind of amazed by this.
Help?</div> | {
"assignee": "cscheid",
"comments": 11,
"created_at": "2022-08-04T17:05:43Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 1685,
"state": "closed",
"title": "require-ing MathJax fully working in Observerable notebook, but NOT in Quarto ojs cell",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1685"
} |
(This is less important now, but will become more important as quarto development settles.)
There should be a way for extensions to declare the minimum required quarto version in their yaml, and for quarto to check against that. | {
"assignee": "dragonstyle",
"comments": 0,
"created_at": "2022-08-04T14:53:03Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "v1.1",
"number": 1681,
"state": "closed",
"title": "Extensions should be able to declare quarto version requirements",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1681"
} |
Github did not allow me to post the full issue so I will do it in pieces.
Issue #1660 led me to look for a way to include uncited works in a book bibliography, which I am doing by including a text file with the relevant bibtex keys in the #refs div. (A seemingly equivalent approach is to cite those works in a .hidden div.) However, that led to a problem in which citations and the bibliography may not be properly synchronized.
I am not sure of precisely when the problem will occur, but here is a way to produce one circumstance in which it occurs:
- In RStudio, create a new book project.
- Add 2 more Knuth works to the references.bib file. Assume that, in addition to the May 1984 journal article included in the default book project, he had a two-volume technical report put out through ABC Institution called "More Literate Programming", where Volume 1 came out in June 1984 and Volume 2 came out in July 1984. Assume the bibliographic software (Zotero in my case) assigned bibtex keys knuth84b and knuth84a to Volumes 1 and 2 respectively. For my testing purposes I put Volume 2 into the file before Volume 1 but I don't know if that ordering is important. The references.bib file will now look like the code block that I will copy into a subsequent comment.
- Cite Volume 2 (knuth84a) in intro.qmd (in addition to the existing cite of the journal article), but do not cite Volume 1. The relevant line in intro.qmd will now be:
`See @knuth84 and @knuth84a for additional discussion of literate programming.`
- Put the bibtex keys for all 3 works (journal article and 2-volume technical report) in a separate text file, to help implement my workaround to allow a full bibliography in a book. (I would create this file programmatically by reading the references.bib file.) I call the file "all_cited_and_uncited_works.txt". It will look like this:
```
@knuth84
@knuth84a
@knuth84b
```
- Include the file in the references.qmd file, in the #refs div. Here's what my references.qmd file looks like:
```
# References {.unnumbered}
::: {#refs}
{{< include all_cited_and_uncited_works.txt >}}
:::
```
- Render the book. I do this via "quarto render" from the terminal.
- Look at intro.html. You should see the following for the citations
> See Knuth (1984b) and Knuth (1984a) for additional discussion of literate programming.
- Quarto has assigned 1984b to the journal article (1st citation) and 1984a to Volume 2 of the report. While this may seem surprising it is ok as far as I can tell - there's no reason it should have the same year-letter values as the bibtex keys, because quarto should assign them based on appearance in the bibliography, whereas Zotero or other bibliographic software will assign them considering all works by the same author in the particular citation library. Hovering over the hyperlinked 1984b and 1984a values in intro.html shows that they do, indeed, reference the article and Volume 2 report properly.
| {
"assignee": "jjallaire",
"comments": 9,
"created_at": "2022-08-04T11:38:24Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1678,
"state": "closed",
"title": "Citations not properly synchronized with bibliography in certain cases - v.2",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1678"
} |
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1674
<div type='discussions-op-text'>
<sup>Originally posted by **RaymondBalise** August 4, 2022</sup>
When I do `quarto install tool tinytex` I get a message saying:
```bash
(\) Updating Path (inspecting 1 possible paths)WARNING: Unable to determine a path to use when installing TeX Live.
To complete the installation, please run the following:
/Users/me/Library/TinyTeX/bin/universal-darwin/tlmgr option sys_bin <bin_dir_on_path>
```
I don't know what to use for <bin_dir_on_path>. I am guessing that it wants me to type `/Users/me/Library/TinyTeX/bin`. Is that correct or does it want me to type the path to my machine's `/bin` directory?
Currently the quarto docs do not have a section on installing helper tools. The PDF instructions have the line for installing tinytex and the instructions for chromium are buried on the page covering authoring diagrams. Having a page showing how to install/check the addins on Mac, Windows (and perhaps Linux), with the answer to the above question, would be most excellent.
In particular, it would be good to have a gentle introduction (for frightened beginners who don't know what a command line is), dedicated to these lines:
```bash
quarto tools install tinytex
quarto tools install chromium
quarto tools check
```
</div> | {
"assignee": "dragonstyle",
"comments": 1,
"created_at": "2022-08-04T11:38:22Z",
"creator": "dragonstyle",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": "v1.2",
"number": 1677,
"state": "closed",
"title": "Improve Quarto Tools Docs",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1677"
} |
Issue #1660 led me to look for a way to include uncited works in a book bibliography, which I am doing by including a text file with the relevant bibtex keys in the #refs div. (A seemingly equivalent approach is to cite those works in a .hidden div.) However, that led to a problem in which citations and the bibliography may not be properly synchronized.
I am not sure of precisely when the problem will occur, but here is a way to produce one circumstance in which it occurs:
- In RStudio, create a new book project.
- Add 2 more Knuth works to the references.bib file. Assume that, in addition to the May 1984 journal article included in the default book project, he had a two-volume technical report put out through ABC Institution called "More Literate Programming", where Volume 1 came out in June 1984 and Volume 2 came out in July 1984. Assume the bibliographic software (Zotero in my case) assigned bibtex keys knuth84b and knuth84a to Volumes 1 and 2 respectively. For my testing purposes I put Volume 2 into the file before Volume 1 but I don't know if that ordering is important. The references.bib file will now look like the code block copied further below.
- Cite Volume 2 (knuth84a) in intro.qmd (in addition to the existing cite of the journal article), but do not cite Volume 1. The relevant line in intro.qmd will now be:
`See @knuth84 and @knuth84a for additional discussion of literate programming.`
- Put the bibtex keys for all 3 works (journal article and 2-volume technical report) in a separate text file, to help implement my workaround to allow a full bibliography in a book. (I would create this file programmatically by reading the references.bib file.) I call the file "all_cited_and_uncited_works.txt". It will look like this:
```
@knuth84
@knuth84a
@knuth84b
```
- Render the book. I do this via "quarto render" from the terminal.
# references.bib file as revised
```
@article{knuth84,
author = {Knuth, Donald E.},
title = {Literate Programming},
year = {1984},
issue_date = {May 1984},
publisher = {Oxford University Press, Inc.},
address = {USA},
volume = {27},
number = {2},
issn = {0010-4620},
url = {https://doi.org/10.1093/comjnl/27.2.97},
doi = {10.1093/comjnl/27.2.97},
journal = {Comput. J.},
month = may,
pages = {97β111},
numpages = {15}
}
@techreport{knuth84a,
author = {Knuth, Donald E.},
title = { {{More Literate Programming}} {{Volume}} 2},
year = {1984},
month = july,
institution = {{ABC Institution}}
}
@techreport{knuth84b,
author = {Knuth, Donald E.},
title = { {{More Literate Programming}} {{Volume}} 1},
year = {1984},
month = june,
institution = {{ABC Institution}}
}
```
| {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-04T11:10:56Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1675,
"state": "closed",
"title": "Citations not properly synchronized with bibliography in certain cases",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1675"
} |
### Bug description
I am currently trying to explore using Quarto for the Python work I am doing in VSCode, where I had traditionally been using VSCode's version of the Jupyter Notebook (.ipynb).
When I took my notebook, and put in the appropriate YAML raw header cell, everything rendered correctly into HTML -- it looked great!
However, when I tried to do the same code from a .qmd file, it did not work. Specifically, clicking the "render" button kept on referencing the "base" conda environment, when this project was in a different conda environment (with package I did not want to load into the "base" version. For the .ipynb file, there is a button on the top-right with which to change the environment, and then all the options work correctly.
I can still correctly render the qmd file when in the command line, but I would like to run it using the options in the IDE as well. Does anyone know of the best way to deal with this issue?
***
When I click "Render HTML", the terminal seems to run a `conda activate base`, then runs the `quarto preview` , and then (when it fails and exits) runs `conda activate base2` (which is not even the environment I tried to use) ...but when I run it manually in the terminal from within my original project environment, it's fine.
***
I am using VSCode version:
Version: 1.69.2 (Universal)
Commit: 3b889b090b5ad5793f524b5d1d39fda662b96a2a
Date: 2022-07-18T16:12:57.074Z (2 wks ago)
Electron: 18.3.5
Chromium: 100.0.4896.160
Node.js: 16.13.2
V8: 10.0.139.17-electron.0
OS: Darwin x64 21.4.0
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.12 (Conda)
Path: /Users/federaj/miniconda3/envs/base2/bin/python
Jupyter: 4.10.0
Kernels: juliapro_v1.5.3-1-1.5, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Up to date v2022.08 v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-04T02:59:33Z",
"creator": "AlanFeder",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1673,
"state": "closed",
"title": "Issue with Quarto/Python/VSCode/.qmd referencing wrong conda environment",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1673"
} |
Hi!
Trying out quarto today and got the error in the title upon rendering the example document.
Particularly, the error arises on copying 'quarto.js' from the installation path to the document '*_files' directory.
I'm running the quarto version 1.0.37 on Linux Mint 20.3 (which is based on Ubuntu 20.*). My Rstudio version is also quite new since I've just updated it yesterday. I think its worth mention that this error also arises when calling the render from the R console.
I'm really keen on this project and hope I can use this term on the University, but sadly looks there is a lot to polish yet.
Cheers! | {
"assignee": "dragonstyle",
"comments": 9,
"created_at": "2022-08-04T00:44:39Z",
"creator": "emilianomm",
"is_pull_request": false,
"labels": [
"file-systems"
],
"locked": false,
"milestone": "v1.4",
"number": 1672,
"state": "open",
"title": "ERROR: PermissionDenied: Operation not permitted (os error 1)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1672"
} |
(Apologies for the blank initial post, not getting a raw markdown-based template confused the heck out of me!)
### Bug description
When attempting to render scripts involving arrow S3 operations, quarto fails part way through with this error.
```r
download.file("https://github.com/cboettig/forecasts-darts-framework/raw/main/weather-covariates.qmd", "sigpipe.qmd")
quarto::quarto_render("sigpipe.qmd")
# ...
#> $ include: logi FALSE
#>
#>
#> [31moutput file: sigpipe.knit.md
#>
#> [39m[31mError: ignoring SIGPIPE signal
#> Execution halted
#> [39m
#> Error in "processx::run(quarto_bin, args, echo = TRUE)": ! System command 'quarto' failed
```
<sup>Created on 2022-08-03 by the [reprex package](https://reprex.tidyverse.org/) (v2.0.1)</sup>
I understand that this error is at least in some way the fault of `arrow` (see https://issues.apache.org/jira/browse/ARROW-16680?page=com.atlassian.jira.plugin.system.issuetabpanels%3Aall-tabpanel), but quarto's handling of this manages to turn what is usually just a nuisance message into a showstopper. In most other contexts, the code runs without error. Compare the execution of the same commands, but with:
- `rmarkdown::render()` : no error
- callr::rscript() : no error
- RScript - throws an error
- knit button in RStudio -- throws the error, but continues to pandoc rendering of the html, so is less problematic
- littler `r`: no error (because unlike R, it can handle a SIGPIPE)
I don't fully understand why arrow throws a SIGPIPE (sometimes?) in it's finalizers here, or why some R tools choose to treat SIGPIPE as an error, but this is rather annoying. (especially as just about every day I want to show someone the awesomeness of quarto and arrow, and so hitting a opaque error is embarrassing! :face_exhaling: ).
### `quarto check` Output
```
quarto check
[β] Checking Quarto installation......OK
Version: 0.9.613
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.10
Path: /home/cboettig/cboettig/forecasts-darts-framework/venv/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.0
Path: /usr/local/lib/R
LibPaths:
- /usr/local/lib/R/site-library
- /usr/local/lib/R/library
- /home/cboettig/cboettig/forecasts-darts-framework/renv/library/R-4.2/x86_64-pc-linux-gnu
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
quarto tools check
(/) Inspecting toolsDownload https://deno.land/x/[email protected]/directories.ts
(|) Inspecting toolsDownload https://deno.land/x/[email protected]/deps.ts
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex External Installation --- v2022.08
```
RStudio Server: 2022.02.3 Build 492
(Running in Ubuntu 20.04, e.g. in rocker/geospatial container RStudio instance, but error can also be reproduced in other environments, including on any OS in GH-Actions. )
```
β Session info βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
setting value
version R version 4.2.1 (2022-06-23)
os Ubuntu 20.04.4 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Etc/UTC
date 2022-08-03
rstudio 2022.07.0+548 Spotted Wakerobin (server)
pandoc 2.18 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)
β Packages βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
package * version date (UTC) lib source
arrow * 8.0.0 2022-05-09 [1] RSPM (R 4.2.0)
assertthat 0.2.1 2019-03-21 [2] RSPM (R 4.2.0)
bit 4.0.4 2020-08-04 [2] RSPM (R 4.2.0)
bit64 4.0.5 2020-08-30 [2] RSPM (R 4.2.0)
bslib 0.4.0 2022-07-16 [1] CRAN (R 4.2.0)
cachem 1.0.6 2021-08-19 [2] RSPM (R 4.2.0)
callr 3.7.1 2022-07-13 [1] CRAN (R 4.2.0)
cli 3.3.0 2022-04-25 [2] RSPM (R 4.2.0)
crayon 1.5.1 2022-03-26 [2] RSPM (R 4.2.0)
DBI 1.1.3 2022-06-18 [1] RSPM (R 4.2.0)
devtools 2.4.4 2022-07-20 [1] RSPM (R 4.2.0)
digest 0.6.29 2021-12-01 [2] RSPM (R 4.2.0)
dplyr 1.0.9 2022-04-28 [1] RSPM (R 4.2.0)
ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.2.0)
evaluate 0.15 2022-02-18 [2] RSPM (R 4.2.0)
fansi 1.0.3 2022-03-24 [2] RSPM (R 4.2.0)
fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.2.0)
fs 1.5.2 2021-12-08 [2] RSPM (R 4.2.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
glue 1.6.2 2022-02-24 [2] RSPM (R 4.2.0)
hms 1.1.1 2021-09-26 [2] RSPM (R 4.2.0)
htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0)
htmlwidgets 1.5.4 2021-09-08 [2] RSPM (R 4.2.0)
httpuv 1.6.5 2022-01-05 [2] RSPM (R 4.2.0)
jquerylib 0.1.4 2021-04-26 [2] RSPM (R 4.2.0)
jsonlite 1.8.0 2022-02-22 [2] RSPM (R 4.2.0)
knitr 1.39 2022-04-26 [2] RSPM (R 4.2.0)
later 1.3.0 2021-08-18 [2] RSPM (R 4.2.0)
lattice 0.20-45 2021-09-22 [3] CRAN (R 4.2.1)
lifecycle 1.0.1 2021-09-24 [2] RSPM (R 4.2.0)
magrittr 2.0.3 2022-03-30 [2] RSPM (R 4.2.0)
Matrix 1.4-1 2022-03-23 [3] CRAN (R 4.2.1)
memoise 2.0.1 2021-11-26 [2] RSPM (R 4.2.0)
mime 0.12 2021-09-28 [2] RSPM (R 4.2.0)
miniUI 0.1.1.1 2018-05-18 [2] RSPM (R 4.2.0)
neon4cast 0.1.0 2022-07-25 [1] Github (eco4cast/neon4cast@3ea5c2e)
pillar 1.8.0 2022-07-18 [1] CRAN (R 4.2.0)
pkgbuild 1.3.1 2021-12-20 [2] RSPM (R 4.2.0)
pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.2.0)
pkgload 1.3.0 2022-06-27 [2] RSPM (R 4.2.0)
png 0.1-7 2013-12-03 [2] RSPM (R 4.2.0)
prettyunits 1.1.1 2020-01-24 [2] RSPM (R 4.2.0)
processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.0)
profvis 0.3.7 2020-11-02 [1] RSPM (R 4.2.0)
promises 1.2.0.1 2021-02-11 [2] RSPM (R 4.2.0)
ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0)
purrr 0.3.4 2020-04-17 [2] RSPM (R 4.2.0)
R6 2.5.1 2021-08-19 [2] RSPM (R 4.2.0)
Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0)
read4cast 0.0.2 2022-07-29 [1] Github (eco4cast/read4cast@28829bf)
readr 2.1.2 2022-01-30 [2] RSPM (R 4.2.0)
remotes 2.4.2 2021-11-30 [2] RSPM (R 4.2.0)
renv 0.15.5 2022-05-26 [1] RSPM (R 4.2.0)
reprex 2.0.1 2021-08-05 [2] RSPM (R 4.2.0)
reticulate 1.25 2022-05-11 [1] CRAN (R 4.2.0)
rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.0)
rmarkdown 2.14 2022-04-25 [2] RSPM (R 4.2.0)
rstudioapi 0.13 2020-11-12 [2] RSPM (R 4.2.0)
sass 0.4.2 2022-07-16 [1] CRAN (R 4.2.0)
score4cast 0.0.0.9000 2022-07-29 [1] Github (eco4cast/score4cast@2a6673d)
sessioninfo 1.2.2 2021-12-06 [2] RSPM (R 4.2.0)
shiny 1.7.2 2022-07-19 [1] RSPM (R 4.2.0)
stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0)
stringr 1.4.0 2019-02-10 [2] RSPM (R 4.2.0)
tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
tidyselect 1.1.2 2022-02-21 [2] RSPM (R 4.2.0)
tzdb 0.3.0 2022-03-28 [2] RSPM (R 4.2.0)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.0)
usethis 2.1.6 2022-05-25 [1] RSPM (R 4.2.0)
utf8 1.2.2 2021-07-24 [2] RSPM (R 4.2.0)
vctrs 0.4.1 2022-04-13 [2] RSPM (R 4.2.0)
withr 2.5.0 2022-03-03 [2] RSPM (R 4.2.0)
xfun 0.31 2022-05-10 [1] RSPM (R 4.2.0)
xtable 1.8-4 2019-04-21 [2] RSPM (R 4.2.0)
yaml 2.3.5 2022-02-21 [2] RSPM (R 4.2.0)
[1] /home/cboettig/R/x86_64-pc-linux-gnu-library/4.2
[2] /usr/local/lib/R/site-library
[3] /usr/local/lib/R/library
```
### Checklist
- [x] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [x] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [x] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 11,
"created_at": "2022-08-03T20:41:48Z",
"creator": "cboettig",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1667,
"state": "closed",
"title": "quarto erroneously halts with error: Error: ignoring SIGPIPE signal",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1667"
} |
# What?
I'd like Quarto to create _all_ temporary/intermediate files in the given subdirectory of the project root (or `/tmp`, or another user-provided directory). By "intermediate files" I mean all files that Quarto manages itself: `.aux`, `.tex`, `.log`, the intermediate `.pdf`, the `.md` generated from the `.qmd` and so on.
I'd like to write something like this in the frontmatter:
```
project:
output-temp-dir: temporary_files
output-dir: out
```
This would make Quarto write stuff _only_ to `output-dir` and `output-temp-dir` and nowhere else. Currently, like knitr/bookdown/Rmarkdown, Quarto will write temporary files to the current directory.
# Why?
1. I created a Quarto project with the default file `report.qmd` (Quarto markdown).
2. I tried editing it in RStudio but didn't like it, so I exited RStudio _without closing the file_.
3. I switched to Zettlr, but it couldn't see the file, so I renamed it to `report.md` (regular Markdown). Now it worked and I continued working on `report.md` for a week in Zettlr.
4. Rendering the file with `quarto render --to pdf` worked great. I simply had to put `project: render: report.md` in `_quarto.yml`.
5. Today I started RStudio and apparently saved `report.qmd` (Quarto markdown!), so that it appeared in my project. Now I had _both_ `report.md` with a week's worth of work and the almost empty `report.qmd`. For whatever reason (again, probably RStudio re-saved the old version of `_quarto.yml` too) the line `project: render: report.md` got changed to `.qmd`.
6. I finally finished my work on `report.md` and rendered it: `quarto render --to pdf`.
7. `report.md` was __GONE__ and `report.pdf` contained whatever nonsense `report.qmd` had.
8. I attempted to recover `report.md` with various tools, but to no avail.
It looks like in the process of analyzing `report.qmd`, Quarto deleted the "old" `report.md`, created a _new_ `report.md` with the processed contents of `report.qmd`, merrily created the PDF from that MD file and then deleted `report.md` as an artefact of processing `report.qmd`.
Now all my work is gone, and it's kinda my fault because I named my file `report.md` and had a `report.qmd` alongside it. Also, I could've easily used version control, but deliberately chose not to since I was too lazy to set it up. Which turned out to be a stupid decision. It's also Quarto's fault: it could've looked at the modification dates, wondered why the "temporary" file `report.md` is _much newer_ than the "original" `report.qmd` and asked me for permission to overwrite `report.md`.
---------
I would like Quarto (and knitr/bookdown/RMarkdown/whatever) to do its processing and creating temporary files __in `/tmp`__, because that's where _temporary_ files are supposed to go. Or in `output-temp-dir: temporary_files`, as suggested earlier, so that the user can control where the temporary files are going. But _not_ in my working directory, where it can overwrite any important `.md` file I spent a week working on.
That would solve all such problems: I write my MD files in my project's directory, Quarto copies everything to `/tmp/whatevergibberish`, processes it and puts the output into `output-dir`. If the project's settings (or the frontmatter) require to save the `.tex` file, then copy it into the output directory as well. This way, the user doesn't have to worry about the processing done by Quarto. They also don't need to worry about Quarto overwriting their `.md` files.
Also, all output _only_ goes to `output-dir` and Quarto _never ever writes to the directory with the user's source files_ or any other directory besides those marked as `output-`: `output-temp-dir` and `output-dir`. | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-03T19:16:38Z",
"creator": "ForceBru",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1666,
"state": "open",
"title": "[Feature request] Can Quarto please create_all_ temporary files _not_ in the same directory with my source files?",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1666"
} |
### Bug description
It seems "Published document" shows a wrong URL (quartopub\.org doesn't exist).
```
$ /c//Users/Yutani/AppData/Local/Programs/Quarto/bin/quarto.cmd publish quarto-pub ./quarto_test.qmd
...snip...
[>] Preparing to publish document
[>] Uploading files (complete)
[>] Deploying published document
[>] Published document: https://quartopub.org/sites/yutani/quarto_test
[>] Account site updated: https://yutani.quarto.pub
```
### `quarto check` Output
```bash
$ /c//Users/Yutani/AppData/Local/Programs/Quarto/bin/quarto.cmd check
[>] Checking Quarto installation......OK
Version: 1.0.37
Path: C:\Users\Yutani\AppData\Local\Programs\Quarto\bin\
CodePage: 932
[>] 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:/PROGRA~1/R/R-42~1.1
LibPaths:
- C:/Users/Yutani/AppData/Local/R/win-library/4.2
- C:/Program Files/R/R-4.2.1/library
rmarkdown: 2.14
[>] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
$ /c//Users/Yutani/AppData/Local/Programs/Quarto/bin/quarto.cmd tools check
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-03T14:02:43Z",
"creator": "yutannihilation",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1662,
"state": "closed",
"title": "The result of \"quarto publish quarto-pub\" shows a wrong URL.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1662"
} |
Hi,
First, thanks so much for making this wonderful tool. I've been an active RMarkdown user, while also working heavily with a VS Code and Python. I'm very excited to see there's a RMarkdown equivalent outside R ecosystem, finally.
I intend to use Quarto with only Python and VS Code on macOS. After using [homebrew](https://formulae.brew.sh/cask/quarto#default) to install `quarto`, which is the same as installing with the `quarto-1.0.37-macos.pkg` file, my shell can't find `quarto` in the PATH.
```
$ quarto
zsh: command not found: quarto
```
After some digging, I discovered that `quarto-1.0.37-macos.pkg` installed `quarto` folder in `/Applications`. A simple solution would be adding `Applications/quarto/bin` into my PATH. However, what I believe is a more elegant solution is following other command line tool installations such as [youtube-dl](https://github.com/Homebrew/homebrew-core/blob/HEAD/Formula/youtube-dl.rb).
For whomever facing the similar problem and also uses homebrew on macOS, I moved `/Applications/quarto` to `/opt/homebrew/Cellar/quarto`. Then I added the symbolic link of `quarto` to `/opt/homebrew/bin/` using the following command (you can also just create a symbolic link without moving):
```
ln -s /opt/homebrew/Cellar/quarto/bin/quarto /opt/homebrew/bin/quarto
```
Now my shell can successfully pick `quarto` up.
<img width="727" alt="quarto" src="https://user-images.githubusercontent.com/20390106/182623638-ec1d69b4-a747-440b-b7fd-0db88aa63e38.png"> | {
"assignee": "dragonstyle",
"comments": 6,
"created_at": "2022-08-03T13:47:28Z",
"creator": "iewaij",
"is_pull_request": false,
"labels": [
"bug",
"installers"
],
"locked": false,
"milestone": "v1.4",
"number": 1661,
"state": "open",
"title": "Improve MacOS Installer Path Handling",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1661"
} |
I would like a bibliography that includes many works that may not be referenced specifically. I am using quarto 1.0.37 for Windows, with the latest Wakerobin build of RStudio.
The [quarto documentation](https://quarto.org/docs/authoring/footnotes-and-citations.html) appears to say I can do this by creating a "dummy nocite metadata field" that either has specific references, or all of them. This mirrors the [pandoc user guide](https://quarto-dev.github.io/quarto-gallery/articles/pdf/pandoc-user-guide.pdf), p.101.
I have created such a metadata field and tried putting it everywhere - at the top of my `references.qmd` file, after the header of the file, inside the fenced `{#refs}` part of the file, in a different .qmd file, and as metadeta in my _quarto.yml file, but the uncited works never show in the references list. This is true whether I put specific references (e.g, @item1, @item2) or the wild card for all works (@*) in the metadata field.
Would it be possible to tell me if I am doing something wrong (and how to do it correctly)?
--------------------- Aside -----------------------------------------------------------
FWIW, I found a way to work around this by creating a separate text file with the list of uncited works (constructed with an R program that reads the .bib file of all works) like this:
```
::: {#refs}
{{< include all_cited_and_uncited_works.qmd >}}
:::
```
However, this is not a great solution because when there are multiple works by the same author, where some of them are cited, it is hard to get the sort order of this list synchronized with the works as they appear in the resulting html -- some works in the body of the book will link to the wrong works in the references html file. So I'd rather not try to use this workaround.
| {
"assignee": "jjallaire",
"comments": 8,
"created_at": "2022-08-03T12:33:52Z",
"creator": "donboyd5",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.1",
"number": 1660,
"state": "closed",
"title": "cannot get nocite to work",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1660"
} |
### Bug description
** THIS MIGHT BE RELATED TO ISSUE:** https://github.com/quarto-dev/quarto-cli/issues/909#issue-1238560733
When attempting to preview or render a QMD file with a PDF format output, quarto attempts to update packages in TeX Live and fails to do it. The following is a minimal example that gives the error
I have checked with RStudio and I receive the same error (with a different QMD file of course). This is a bug on quarto
~~~
---
title: TLMGR Problems
format: pdf
---
**Hello World!**
```{python}
d="Hello World!"
```
~~~
```
% quarto preview minimaltest.qmd
Starting python3 kernel...Done
Executing 'minimaltest.ipynb'
Cell 1/1...Done
pandoc
to: latex
output-file: minimaltest.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: TLMGR Problems
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- missing packages (automatic installation failed)
```
This behavior does not show up when the output is changed from PDF to HTML
```
quarto preview minimaltest.qmd
Starting python3 kernel...Done
Executing 'minimaltest.ipynb'
Cell 1/1...Done
pandoc
to: html
output-file: minimaltest.html
standalone: true
section-divs: true
html-math-method: mathjax
wrap: none
default-image-extension: png
metadata
document-css: false
link-citations: true
date-format: long
lang: en
title: TLMGR Problems
Output created: minimaltest.html
Watching files for changes
Browse at http://localhost:4853/
```
My setup is as following:
OS: OS X 11.6.8
account: user has sudo privileges (but it is not the admin)
quarto: 1.0.37
conda: 4.13.0
python: 3.10.5
Julia: 1.7.3
jupyter:
- jupyter 1.0.0 py310h2ec42d9_7 conda-forge
- notebook 6.4.12 pyha770c72_0 conda-forge
- jupyter_client 7.3.4 pyhd8ed1ab_0 conda-forge
- jupyter_console 6.4.4 pyhd8ed1ab_0 conda-forge
- jupyter_core 4.11.1 py310h2ec42d9_0 conda-forge
- jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge
- jupyterlab_widgets 1.1.1 pyhd8ed1ab_0 conda-forge
nbconvert:
- nbconvert 6.5.0 pyhd8ed1ab_0 conda-forge
- nbconvert-core 6.5.0 pyhd8ed1ab_0 conda-forge
- nbconvert-pandoc 6.5.0 pyhd8ed1ab_0 conda-forge
- nbformat 5.4.0 pyhd8ed1ab_0 conda-forge
tlmgr:
- tlmgr revision 63068 (2022-04-18 07:58:07 +0200)
- tlmgr using installation: /usr/local/texlive/2022
- TeX Live (https://tug.org/texlive) version 2022
tlmgr has been updated by using the utility provided by MacTeX 2022: TeX Live Utility.app, all packages has been updated.
The same behavior appear is instead of having the full MacTeX 2022 distribution (TeX Live) I have the tinyTeX.
Quarto has been installed locally and globally and in both cases the result is the same
To preview I have attempted to prepend the command with **sudo** but the result is the same. All of these has been run in a terminal. Finally I am attaching the output run with the **--verbose** option
```
(quarto) heberto@kepler quarto % quarto preview minimaltest.qmd --verbose
Starting python3 kernel...Done
Executing 'minimaltest.ipynb'
Cell 1/1...Done
pandoc --verbose
to: latex
output-file: minimaltest.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: TLMGR Problems
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/template.patched from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/template.patched
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/doc-class.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/doc-class.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/pandoc.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/pandoc.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/tightlist.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/tightlist.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/tables.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/tables.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/graphics.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/graphics.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/citations.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/citations.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/title.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/title.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/before-body.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/before-body.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/toc.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/toc.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/before-bib.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/before-bib.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/biblio.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/biblio.tex
[INFO] Loaded /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/after-body.tex from /var/folders/jm/ljt12vhj31ggqg5dmbfvk6lh0000gn/T/quarto-session373afdca/40df8cf6/e9f0efca/after-body.tex
[INFO] Running filter /Users/heberto/Applications/quarto/share/filters/quarto-init/quarto-init.lua
[INFO] Completed filter /Users/heberto/Applications/quarto/share/filters/quarto-init/quarto-init.lua in 9 ms
[INFO] Running filter /Users/heberto/Applications/quarto/share/filters/authors/authors.lua
[INFO] Completed filter /Users/heberto/Applications/quarto/share/filters/authors/authors.lua in 9 ms
[INFO] Running filter /Users/heberto/Applications/quarto/share/filters/quarto-pre/quarto-pre.lua
[INFO] Completed filter /Users/heberto/Applications/quarto/share/filters/quarto-pre/quarto-pre.lua in 12 ms
[INFO] Running filter /Users/heberto/Applications/quarto/share/filters/crossref/crossref.lua
[INFO] Completed filter /Users/heberto/Applications/quarto/share/filters/crossref/crossref.lua in 9 ms
[INFO] Running filter /Users/heberto/Applications/quarto/share/filters/layout/layout.lua
[INFO] Completed filter /Users/heberto/Applications/quarto/share/filters/layout/layout.lua in 25 ms
[INFO] Running filter /Users/heberto/Applications/quarto/share/filters/quarto-post/quarto-post.lua
[INFO] Completed filter /Users/heberto/Applications/quarto/share/filters/quarto-post/quarto-post.lua in 9 ms
[INFO] Running filter /Users/heberto/Applications/quarto/share/filters/quarto-finalize/quarto-finalize.lua
[INFO] Completed filter /Users/heberto/Applications/quarto/share/filters/quarto-finalize/quarto-finalize.lua in 7 ms
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- missing packages (automatic installation failed)
```
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Users/heberto/Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.5 (Conda)
Path: /Users/heberto/opt/miniconda3/envs/quarto/bin/python
Jupyter: 4.11.1
Kernels: julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 4,
"created_at": "2022-08-03T12:00:53Z",
"creator": "hebertodelrio",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1659,
"state": "open",
"title": "Quarto trying to update tlmgr fails",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1659"
} |
### Bug description
Hi, I am preparing a Beamer presentation in Quarto which will be rendered into `.pdf` later. When I include date of the talk and my institute in the YAML, it prints date before the institution in the pdf version. We generally prefer the date after the institution. In the source files of Quarto Beamer presentation, I have seen a source `.tex` file where the author and date fields are embedded together. I guess, for that reason, they get printed out together. I cannot modify the Quarto source files since they are read-only. I would appreciate if this can be fixed. I have another question on how to break long titles into two lines in the YAML too. I would like to thank you very much in advance.
```yaml
---
title: "My talk title"
author: "My name"
institute: "My institute"
date: "August 02, 2022"
mathspec: true # for metropolis theme
execute:
enabled: true
warning: false
error: false
comments:
hypothesis:
theme: clean
format:
beamer:
aspectratio: 32
navigation: horizontal
theme: metropolis
colortheme: crane
colorlinks: true
highlight-style: tango
[question.pdf](https://github.com/quarto-dev/quarto-cli/files/9250720/question.pdf)
editor: visual
---
```
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "dragonstyle",
"comments": 3,
"created_at": "2022-08-03T11:04:13Z",
"creator": "gulinan",
"is_pull_request": false,
"labels": [
"bug",
"enhancement",
"early-in-release"
],
"locked": false,
"milestone": "v1.4",
"number": 1658,
"state": "open",
"title": "Add Support for Beamer Template Partials",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1658"
} |
I'm looking to potentially use multiple figure environments, so that one set of figures can be referenced and numbered as usual (e.g. Figure 1, Figure 2 etc) but also allow for an additional set of numbered figures such as schemes (Scheme 1, Scheme 2 etc..).
The desired result is something like in this manuscript where chemical diagrams are labelled separately as Schemes to the rest of the figures: https://api.research-repository.uwa.edu.au/ws/portalfiles/portal/142280159/manuscript.pdf
EDIT: I have been able to utilise multiple environments inside of LaTeX to have both he Figure & Scheme labelling / numbering to be separate (using `\usepackage{chemstyle}`) but it would be great to try and have a similar functionality available for the HTML output as well.
| {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-08-03T01:03:05Z",
"creator": "BradyAJohnston",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 1655,
"state": "open",
"title": "Multiple Figure Numbering Environments",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1655"
} |
While running the tutorial for running Quarto in VSCode, after having installed the quarto.msi package, and the VS code quarto extension, the render step fails with a "Quarto Installation not Found" popup. Of course attempting to re-install quarto results in a "do you want to remove quarto" message.
I assume this is a path problem that was not updated by the install -- but you may want to verify and document this.
I run VSCode typically from the WSL unbuntu shell, but in this case I ran it from "in windows", so it defaults to powershell for the terminal. | {
"assignee": "jjallaire",
"comments": 6,
"created_at": "2022-08-02T22:07:08Z",
"creator": "jmagosta",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1882,
"state": "open",
"title": "Quarto and R paths not found ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1882"
} |
### Bug description
OJS blocks starting on empty lines misbehave in different ways:
- The empty line is reflected on the `echo` output
- The empty line causes the ojs runtime to throw during initialization, which means some of the dynamic CSS fixups don't happen
Minimal repro for both issues:
---
format: html
---
```{ojs}
5 * 5
```
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 99.9.9
Path: /Users/cscheid/repos/github/quarto-dev/quarto-cli/package/dist/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.12
Path: /Users/cscheid/venvs/3_9_5/bin/python3
Jupyter: 4.7.1
Kernels: julia-1.7, python3, c
(|) Checking Jupyter engine render....Exception ignored in: <function BaseEventLoop.__del__ at 0x103d22430>
Traceback (most recent call last):
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/base_events.py", line 688, in __del__
self.close()
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/unix_events.py", line 58, in close
super().close()
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/selector_events.py", line 87, in close
self._close_self_pipe()
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/selector_events.py", line 94, in _close_self_pipe
self._remove_reader(self._ssock.fileno())
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/asyncio/selector_events.py", line 272, in _remove_reader
key = self._selector.get_key(fd)
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 191, in get_key
return mapping[fileobj]
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 72, in __getitem__
fd = self._selector._fileobj_lookup(fileobj)
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 226, in _fileobj_lookup
return _fileobj_to_fd(fileobj)
File "/usr/local/Cellar/[email protected]/3.9.12_1/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 42, in _fileobj_to_fd
raise ValueError("Invalid file descriptor: {}".format(fd))
ValueError: Invalid file descriptor: -1
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Up to date 869685 869685
tinytex Update available v2022.07 v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-08-02T18:44:36Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1648,
"state": "closed",
"title": "problems with OJS blocks starting on empty lines",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1648"
} |
### Bug description
Table captions and references do not render in the HTML document when using Jupyter Lab. Also, the code will still appear even if using `echo: false`.
I'm using MacOS Monterrey 12.4 (M1)
````md
```header
---
title: 'Table Issue'
author: 'Phil Patton'
number-sections: false
highlight-style: pygments
format:
html:
code-fold: true
self-contained: true
jupyter: python3
reference-location: margin
citation-location: margin
---
```
```py
#| label: tbl-planets
#| tbl-cap: Planets
#| echo: false
from IPython.display import Markdown
from tabulate import tabulate
table = [["Sun",696000,1989100000],
["Earth",6371,5973.6],
["Moon",1737,73.5],
["Mars",3390,641.85]]
Markdown(tabulate(
table,
headers=["Planet","R (km)", "mass (x 10^29 kg)"]
))
```
````
<img width="858" alt="Screen Shot 2022-08-02 at 8 20 09 AM" src="https://user-images.githubusercontent.com/15240814/182445908-8f5c1bca-270e-4ea7-a8da-ce1f444cac94.png">
### `quarto check` Output
```bash
[β] Checking Python 3 installation....OK
Version: 3.10.5 (Conda)
Path: /Users/philtpatton/miniforge3/envs/hws/bin/python
Jupyter: 4.10.0
Kernels: python3
[β] Checking Jupyter engine render....OK
```
### `quarto tools check` Output
```bash
(/) Inspecting toolsDownload https://deno.land/x/[email protected]/directories.ts
(|) Inspecting toolsDownload https://deno.land/x/[email protected]/deps.ts
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 1,
"created_at": "2022-08-02T18:23:21Z",
"creator": "philpatton",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1646,
"state": "closed",
"title": "Issue with table captions, references in Jupyter Lab",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1646"
} |
I'd like to make a custom theme which adds a logo to the top left and/or right corners of every `revealjs` slide. I see this [example](https://reveal-hugo.dzello.com/logo-example/#) with [Hugo](https://github.com/dzello/reveal-hugo/blob/master/exampleSite/content/logo-example/_index.md). Is there any way to do this with `quarto`?
I know editing the HTML after `quarto render` is an option, but ideally I'd like to be able to do this all from a custom theme, or something similar, and I don't think that's possible without creating the proper `div` & other elements first.
Love the project! | {
"assignee": "cderv",
"comments": 3,
"created_at": "2022-08-02T17:10:18Z",
"creator": "jcarpi",
"is_pull_request": false,
"labels": [
"enhancement",
"revealjs"
],
"locked": false,
"milestone": "v1.4",
"number": 1883,
"state": "open",
"title": "Adding logos to all `revealjs` slides",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1883"
} |
See https://github.com/quarto-ext/fontawesome/issues/13
Sometimes we want to resolve shortcodes differently (or not at all) depending on the context that the shortcode was called. This isn't possible right now. | {
"assignee": null,
"comments": 0,
"created_at": "2022-08-02T14:56:54Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1644,
"state": "open",
"title": "Capture context of shortcode invocation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1644"
} |
### Bug description
Quarto 1.0.37 returns the following error when trying the sample *.qmd available from https://quarto.org/docs/computations/julia.html
`[Errno 2] No such file or directory: '/Applications/Julia-1.7.app/Contents/Resources/julia/bin/julia'
`
on a macOs, where Julia has been installed with JuliaUp and where the latter has been installed with Home-brew.
Julia's executable (/usr/local/bin/julia) is indeed in the PATH and it correctly points to JuliaUp.
`
/usr/local/bin/julia -> ../Cellar/juliaup/1.6.12/bin/Julia
`
Note that JuliaUp is soon becoming the standard/preferred method of installing Julia.
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.13
Path: /usr/local/opt/[email protected]/bin/python3.9
Jupyter: 4.7.1
Kernels: julia-1.6, julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-02T14:50:39Z",
"creator": "mgiugliano",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1643,
"state": "closed",
"title": "Unexpected Julia path (macOs, using brew and juliaup)",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1643"
} |
### Bug description
Related to #1246, `quarto publish gh-pages`does not respect `output-dir: _site`
instead renders to `./`.
`_quarto.yml` [full [here](https://github.com/eyayaw/eyayaw.github.io/blob/gh-pages/_quarto.yml)]
```yml
project:
type: website
output-dir: _site
```
The last `quarto publish` call results can be seen [here](https://github.com/eyayaw/eyayaw.github.io/tree/gh-pages)
```
~/G/eyayaw.github.io (main)> quarto publish gh-pages
```
````
? Update site at https://Eyayaw.github.io/eyayaw.github.io/? (Y/n) βΊ Yes
From https://github.com/Eyayaw/eyayaw.github.io
* branch gh-pages -> FETCH_HEAD
Rendering for publish:
[1/6] bio.qmd
[2/6] posts/2022-07-31_welcome/index.qmd
[3/6] posts/2022-08-01_ten-baser-tips/index.qmd
[4/6] blog.qmd
[5/6] research.qmd
[6/6] index.qmd
Preparing worktree (resetting branch 'gh-pages'; was at b76bb45)
Branch 'gh-pages' set up to track remote branch 'gh-pages' from 'origin'.
HEAD is now at b76bb45 publish gh-pages
[gh-pages 087d8da] Built site for gh-pages
32 files changed, 6880 insertions(+), 41 deletions(-)
create mode 100644 bio.html
create mode 100644 blog.html
create mode 100644 index.html
create mode 100644 posts/2022-07-31_welcome/index.html
create mode 100644 posts/2022-08-01_ten-baser-tips/index.html
create mode 100644 research.html
create mode 100644 site_libs/bootstrap/bootstrap-dark.min.css
create mode 100644 site_libs/bootstrap/bootstrap-icons.css
create mode 100644 site_libs/bootstrap/bootstrap-icons.woff
create mode 100644 site_libs/bootstrap/bootstrap.min.css
create mode 100644 site_libs/bootstrap/bootstrap.min.js
create mode 100644 site_libs/clipboard/clipboard.min.js
create mode 100644 site_libs/quarto-html/anchor.min.js
create mode 100644 site_libs/quarto-html/popper.min.js
create mode 100644 site_libs/quarto-html/quarto-syntax-highlighting-dark.css
create mode 100644 site_libs/quarto-html/quarto-syntax-highlighting.css
create mode 100644 site_libs/quarto-html/quarto.js
create mode 100644 site_libs/quarto-html/tippy.css
create mode 100644 site_libs/quarto-html/tippy.umd.min.js
create mode 100644 site_libs/quarto-html/zenscroll-min.js
create mode 100644 site_libs/quarto-listing/list.min.js
create mode 100644 site_libs/quarto-listing/quarto-listing.js
create mode 100644 site_libs/quarto-nav/headroom.min.js
create mode 100644 site_libs/quarto-nav/quarto-nav.js
create mode 100644 site_libs/quarto-search/autocomplete.umd.js
create mode 100644 site_libs/quarto-search/fuse.min.js
create mode 100644 site_libs/quarto-search/quarto-search.js
rewrite sitemap.xml (75%)
origin https://github.com/Eyayaw/eyayaw.github.io.git (fetch)
origin https://github.com/Eyayaw/eyayaw.github.io.git (push)
remote: This repository moved. Please use the new location:
remote: https://github.com/eyayaw/eyayaw.github.io.git
To https://github.com/Eyayaw/eyayaw.github.io.git
b76bb45..087d8da HEAD -> gh-pages
[β] Published to https://Eyayaw.github.io/eyayaw.github.io/
To complete publishing, change the source branch for this site to gh-pages.
Set the source branch at: https://github.com/Eyayaw.github.io/eyayaw/Eyayaw.github.io/eyayaw.github.io/settings/page
````
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.4
Path: /usr/bin/python3
Jupyter: 4.10.0
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.0
Path: /opt/R/4.2.0/lib/R
LibPaths:
- /home/eyayaw/R/x86_64-pc-linux-gnu-library/4.2
- /opt/R/4.2.0/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Update available v2022.05 v2022.08
WARNING: TeX Live not on path.
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-02T13:33:46Z",
"creator": "eyayaw",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1640,
"state": "closed",
"title": "`quarto publish gh-pages`does not respect `output-dir: _site`",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1640"
} |
### Bug description
Cross references to section headings are wrong (rendered in-text as a reference to the last appendix with a `#sec id`) when:
- the project is of type book
- when rendering to docx only (pdf and html render correctly)
- the project is using an appendices key in the book config in the _quarto.yml
- there are `#sec ids` in the appendices
- using cross-references to section headings (either chapters or appendices)
Note that the text rendering of the cross reference in the body text is incorrect, but the hyperlink to the section in the document is correct. For example, the cross reference may appear in body text as "Appendix B", but it correctly links to "Chapter 1".
I have attached a zip archive of a book project as an example (created using `quarto create-project word_append_xref --type book`). Note that this cannot be reproduced using a single qmd file.
[word_append_xref.zip](https://github.com/quarto-dev/quarto-cli/files/9238654/word_append_xref.zip)
Source:
```
An xref to the Preface, @sec-one. This should read "Chapter 1".
An xref to the Intro (now Appendix A), @sec-two. This should read "Chapter A", as it
is in the appendices section of the YAML.
Another xref to the Intro (now Appendix A), [Appendix -@sec-two]. This should read "Appendix A",
as it refers to the appendix explicitly and uses the number-only form of cross reference.
An xref to the Summary (now Appendix B), @sec-three. This should read "Chapter B", as it
is in the appendices section of the YAML.
```
Output (created using `quarto render --to docx`):
and with field codes toggled:
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.13
Path: /opt/homebrew/opt/[email protected]/bin/python3.9
Jupyter: 4.10.0
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14.2
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Up to date 869685 869685
tinytex External Installation --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 5,
"created_at": "2022-08-02T02:45:05Z",
"creator": "dan-cloney",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1637,
"state": "closed",
"title": "Cross references for section headings fail when there are appendices and the book is rendered in docx format.",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1637"
} |
### Bug description
Currently, it does not appear like we can run arbitrary R expressions by prefacing the parameter value with !r. Here is an example arbitrary of R expression parameters from the R4DS book (https://r4ds.had.co.nz/r-markdown.html#parameters).
```
---
title: "testing"
format: html
editor: visual
params:
start: !r lubridate::ymd('2015-01-01')
snapshot: !r lubridate::ymd_hms('2015-01-01 12:30:00')
name: "John"
---
```
Running on macOS Monterey Version 12.5
### `quarto check` Output
[β] Checking Quarto installation......OK
Version: 1.0.36
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.9
Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/samparmar/Library/R/4.0/library
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.8
[β] Checking Knitr engine render......OK
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-08-01T16:54:51Z",
"creator": "parmsam",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1629,
"state": "closed",
"title": "Error using arbitrary R expressions in YAML params",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1629"
} |
Hi! I'm following the tutorials but I didn't manage to reproduce the [Computations Tutorial](https://quarto.org/docs/get-started/computations/vscode.html#multiple-figures) plotly 2-column plot.
According to the tutorial I'm supposed to get
<img width="779" alt="image" src="https://user-images.githubusercontent.com/13261989/182183937-81241cac-ece6-469f-8055-0e1f6ec51c35.png">
But when I try it in my computer I get:
<img width="611" alt="image" src="https://user-images.githubusercontent.com/13261989/182184118-02bf109a-9af2-4ba6-a985-e61acfbfe904.png">
I've tried reducing the image size with plotly and increasing the space they can take by using `column: screen` neither method works for me.
<details>
<summary>About Mac</summary>
<img width="229" alt="image" src="https://user-images.githubusercontent.com/13261989/182184677-fa78df84-57c4-4f3d-8230-136738293f89.png">
</details>
<details>
<summary>Quarto check jupyter output</summary>
```
[β] Checking Python 3 installation....OK
Version: 3.8.11 (Conda)
Path: /Users/joaogui1/miniconda3/bin/python
Jupyter: 4.9.1
Kernels: julia-1.7, python3
[β] Checking Jupyter engine render....OK
```
</details>
| {
"assignee": "jjallaire",
"comments": 5,
"created_at": "2022-08-01T15:31:27Z",
"creator": "joaogui1",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1628,
"state": "closed",
"title": "Can't reproduce \"Computations\" Tutorial 2-column plot",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1628"
} |
### Bug description
Setting the mermaid format to svg will result in text inside some diagram boxes being clipped:
````
---
mermaid-format: svg
---
```{mermaid}
graph
L --- P1
L(library)
P1(dashboard <br/> dplyr 0.8.5)
```
````
Allowing the same diagram to be rendered in the browser produces the expected output, as does SVG export from the mermaid live editor:
### `quarto check` Output
```bash
β― quarto check
[β] Checking Quarto installation......OK
Version: 1.1.3
Path: /Users/edavidaja/.local/share/qvm/versions/v1.1.3/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.6
Path: /Users/edavidaja/.pyenv/versions/3.8.6/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.1.2
Path: /Library/Frameworks/R.framework/Versions/4.1/Resources
LibPaths:
- /Users/edavidaja/Library/R/x86_64/4.1/library
- /Library/Frameworks/R.framework/Versions/4.1/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
β― quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 3,
"created_at": "2022-08-01T12:00:37Z",
"creator": "edavidaja",
"is_pull_request": false,
"labels": [
"bug",
"needs-discussion",
"mermaid"
],
"locked": false,
"milestone": "v1.2",
"number": 1622,
"state": "closed",
"title": "`mermaid-format: svg` results in clipping of diagrams",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1622"
} |
### Bug description
calling `quarto render` on a document with an inline style span will present a syntax error in the rendered HTML.
````
```{mermaid}
graph
L --- P1
L(library)
P1("dashboard <br/> <span style='color:red'>dplyr 1.0.5</span>")
```
````
The same document can be rendered and exported correctly by the [mermaid live editor](https://mermaid.ink/svg/pako:eNo1zrEOgkAQBNBf2WyjJoJS2FyQSjsLEtttFm4V4nFHlqMghH8XEu2meJmZGetgBQ2-lfuG_AOSJIEyW9PetZWyTgfyZbYntDw0VWC1kFd6KiAfevYwxMnJdVcHF9So2F1hezcpZOk5veSnzRSEBzxiJ9pxa9etmTwAYWykE0IDW7d-CMkvqxt7y1Huto1B0bzYDXJEHmN4Tr5GE3WUP7q1vP7ufmr5AtJTRD8).
### `quarto check` Output
```bash
β― quarto check
[β] Checking Quarto installation......OK
Version: 1.1.3
Path: /Users/edavidaja/.local/share/qvm/versions/v1.1.3/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.6
Path: /Users/edavidaja/.pyenv/versions/3.8.6/bin/python3
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.1.2
Path: /Library/Frameworks/R.framework/Versions/4.1/Resources
LibPaths:
- /Users/edavidaja/Library/R/x86_64/4.1/library
- /Library/Frameworks/R.framework/Versions/4.1/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
β― quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.08
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-08-01T11:47:12Z",
"creator": "edavidaja",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1621,
"state": "closed",
"title": "Mermaid diagrams with inline styles present syntax error",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1621"
} |
Dear RStudio Quarto developers,
first of all - in general I like a lot what I have seen so far from quarto in RStudio - thanks a lot!
I have a question regarding an unexpected behavior:
If I render a quarto document, identical plots are omitted in a code chunk, while they show up as expected when they are not identical.
I added a minimal example in this repository:
[email protected]:sebastian-gerdes/quarto_plots.git
Thanks a lot for any answer in advance!
Best greetings,
Sebastian (using RStudio 2022.07.1)
| {
"assignee": null,
"comments": 1,
"created_at": "2022-08-01T07:01:38Z",
"creator": "sebastian-gerdes",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1631,
"state": "closed",
"title": "Plots not included as expected in quarto document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1631"
} |
### Bug description
For revtex, `\author` `\title` and etc are included after `\begin{document}`.
But quarto automatically transform `\author` `\title` before `\begin{document}` which causes errors.
It is a general issue for using different `documentclass`
Here is the qmd:
[test.txt](https://github.com/quarto-dev/quarto-cli/files/9230447/test.txt)
### `quarto check` Output
quarto is alright
### `quarto tools check` Output
quarto is alright
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [x] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [x] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [x] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [x] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-08-01T02:35:41Z",
"creator": "Lightup1",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1617,
"state": "closed",
"title": "incompatible with revtex",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1617"
} |
### Bug description
Recreating the exact same code from the [computations tutorial](https://quarto.org/docs/get-started/computations/vscode.html) but using Julia instead of Python breaks the subfigure functionality. Instead of rendering a figure with a main caption and two subcaptions, the first `fig-subcap` is used as the main caption while `fig-cap` is ignored and only the last figure is rendered. Running Pop_OS 22
The minimal example and resulting .pdf are attached below:
[jlhello.pdf](https://github.com/quarto-dev/quarto-cli/files/9229739/jlhello.pdf)
[hello.pdf](https://github.com/quarto-dev/quarto-cli/files/9229740/hello.pdf)
### `quarto check` Output
```bash
β― quarto check
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.2 (Conda)
Path: /home/alonsoc1s/miniconda3/envs/base/bin/python
Jupyter: 4.9.1
Kernels: julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.1.3
Path: /usr/lib/R
LibPaths:
- /home/alonsoc1s/R/x86_64-pc-linux-gnu-library/4.1
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
β― quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-31T21:30:40Z",
"creator": "alonsoC1s",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1616,
"state": "closed",
"title": "Subfigures not supported on Julia",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1616"
} |
### Bug description
When running `quarto render` with the CLI, `README.qmd` files seem to be treated differently from files with other names. I have created minimal `.qmd` documents with nothing other than a top-level header, and the issue persists, so it is not related to the Quarto syntax of the documents. There are a few different scenarios where this occurs:
1. If I have a top-level file named `README.qmd`, running `quarto render` does not render the file. However, if I modify `_quarto.yml` to include
```
project:
render:
- README.qmd
```
then it will render just fine.
2. Even if I modify the `_quarto.yml` file, `README.qmd` files in lower-level directories are not rendered. This doesn't appear to be a globbing issue, as I've tried a few different wildcards.
Perhaps this is desired behavior, but it does not seem to be documented on the Quarto Projects page. It seems that rendering a bunch of README files in GFM for various subdirectories of a GitHub repo is a reasonable use case, so I think others may run into this issue in the future.
If this is indeed desired behavior, a simple workaround I've found is to name the Quarto file something like `read_me.qmd` and include `output-file: README.md` in the YAML header.
I am running this on MacOS Monterey 12.4.
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.9.13
Path: /usr/local/opt/[email protected]/bin/python3.9
Jupyter: (None)
Jupyter is not available in this Python installation.
Install with python3 -m pip install jupyter
[β] Checking R installation...........OK
Version: 4.2.1
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Users/MJ/R_Packages_4.1
- /Library/Frameworks/R.framework/Versions/4.2/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "jjallaire",
"comments": 5,
"created_at": "2022-07-31T21:11:51Z",
"creator": "MCMaurer",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "Future",
"number": 1615,
"state": "open",
"title": "Can't render README.qmd by default or recursively",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1615"
} |
### Bug description
When using Julia and rendering to PDF the figures in the final PDF are raster images instead of the vector graphics that R and Python produce by default. I tried fixing this with
```md
format:
pdf:
default-image-extension: tex
```
but the issue persists.
Is this expected behaviour?
Is there a way to fix this?
Why is Julia the only language that does not output vector images by default?
I'm rendering the basic file found in [the Julia tutorial](https://quarto.org/docs/computations/julia.html#overview)
I'm on Pop_OS (22) Linux, kernel 5.17.15 generic
### `quarto check` Output
```bash
β― quarto check
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /opt/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.10.2 (Conda)
Path: /home/-/miniconda3/envs/test/bin/python
Jupyter: 4.9.1
Kernels: julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.1.3
Path: /usr/lib/R
LibPaths:
- /home/-/R/x86_64-pc-linux-gnu-library/4.1
- /usr/local/lib/R/site-library
- /usr/lib/R/site-library
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
β― quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 3,
"created_at": "2022-07-31T19:24:24Z",
"creator": "alonsoC1s",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1614,
"state": "closed",
"title": "PDF output for Julia produces raster instead of vector graphics for plots",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1614"
} |
### Bug description
I generated a blog project with the default quarto command on MacOS 12.3. Then I added some Julia code to `posts/welcome/index.qmd` such that it reads:
````qmd
---
title: "Welcome To My Blog"
author: "Tristan O'Malley"
date: "2022-07-27"
categories: [news]
jupyter: julia-1.7
---
This is the first post in a Quarto blog. Welcome!
Since this post doesn't specify an explicit `image`, the first image in the post will be used in the listing page of posts.
### Dependencies:
```{julia}
using Pkg
1+2
Pkg.status()
```
````
When I run `quarto preview . --execute-debug` from the root folder and make a change and save, I see this each time:
```
[1/2] posts/welcome/index.qmd
- Checking for existing kernel
- No existing kernel found
Starting julia-1.7 kernel...- Executing notebook with oneshot kernel
```
The start of the kernel takes 30+ seconds each time so that's not great of course.
If I do `quarto preview posts/welcome/index.qmd --execute-debug` the same behavior occurs.
However, when I remove the `_quarto.yml` in the root folder and then do `quarto preview posts/welcome/index.qmd --execute-debug`, the output is:
```
- Connecting to kernel
Starting julia-1.7 kernel...2022-07-31 20:31:26,974 - root - Level 25 - starting notebook server subprocess
2022-07-31 20:31:26,974 - root - Level 25 - starting notebook server subprocess
2022-07-31 20:31:27,161 - root - Level 25 - running notebook server subprocess
2022-07-31 20:31:27,162 - root - Level 25 - creating notebook server (tcp: /Users/.../Library/Caches/quarto/jt/4c2f75fc67df95bfca68)
2022-07-31 20:31:27,166 - root - Level 25 - notebook server bound to port 61231
2022-07-31 20:31:27,324 - root - Level 25 - handling server request
- Kernel connection successful
- Sending execute command to kernel
- Execute command sent, reading response
2022-07-31 20:31:27,326 - root - Level 25 - executing notebook
Done
Executing 'index.ipynb'
Cell 1/1...Done
- Server request complete
```
After that, I can make changes and the update is very fast, the existing kernel is found.
I assumed it would be no problem to use blog mode with persistent Julia kernels, am I doing something wrong?
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.9
Path: /Library/Developer/CommandLineTools/usr/bin/python3
Jupyter: 4.11.1
Kernels: julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-31T18:50:19Z",
"creator": "jkrumbiegel",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1613,
"state": "closed",
"title": "Website mode seems to prohibit persistent Julia kernels",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1613"
} |
### Bug description
If I specify `number-sections: false` in my yaml header for a quarto book and render to a narrow HTML page the chapter number shows up in the table of contents at the top of the page.
To see the bug, make the default book project with the RStudio IDE (I am using 2022.07.0 Build 548 on a Mac running macOS Monterey Version 12.4). Add the `number-sections` statement to the html section:
```
project:
type: book
book:
title: "resize_bug"
author: "Jane Doe"
date: "7/31/2022"
chapters:
- index.qmd
- intro.qmd
- summary.qmd
- references.qmd
bibliography: references.bib
format:
html:
theme: cosmo
number-sections: false
pdf:
documentclass: scrreprt
```
Then make the page narrow enough to show the table of contents at the top of the page and go to the introduction or summary chapters. On a wide display the chapter numbers are suppressed but on a narrow page they appear. I see this in the IDE and on Brave (Version 1.41.100 Chromium: 103.0.5060.134 (Official Build) (arm64)).
### `quarto check` Output
```bash
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.9
Path: /Applications/Xcode.app/Contents/Developer/usr/bin/python3
Jupyter: 4.11.1
Kernels: python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.0
Path: /Library/Frameworks/R.framework/Resources
LibPaths:
- /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```bash
[β] Inspecting tools
Tool Status Installed Latest
chromium Up to date 869685 869685
tinytex Up to date v2022.07 v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-31T16:20:40Z",
"creator": "RaymondBalise",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1611,
"state": "closed",
"title": "`number-sections: false` in _quarto.yml for a HTML book does not work consistently",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1611"
} |
https://github.com/quarto-dev/quarto-web/blob/bb8763a1c5164c2ac9b5b72188747e286fe34cc2/docs/projects/quarto-projects.qmd#L70
I would suggest **command line**. It was not directly clear to me looking at the code chunk that you meant bash.
While we are on the subject, why doesn't hitting the render button on a single page incorporate the _quarto.yml? My revealjs presentation renders to html doc when hitting the render button. While running quarto render-project in bash works as excpected. | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-31T15:54:30Z",
"creator": "ShKlinkenberg",
"is_pull_request": false,
"labels": [
"needs-repro"
],
"locked": false,
"milestone": null,
"number": 1632,
"state": "closed",
"title": "Command line bold",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1632"
} |
In the [Creating Citeable Articles](https://quarto.org/docs/authoring/create-citeable-articles.html#google-scholar) the metadata compatible with Google Scholar is listed. The set of metadata tags accepted by Google Scholar is a subset of a more general open standard parsed by [Zotero](https://www.zotero.org/support/dev/exposing_metadata) based on Highwire vocabulary. If metadata is done properly, Zotero browser plug-in will be able to generate proper record from the Quarto article.
I suggest we expand the list of metadata included in the `google-scholar` partial or add a new partial called `zotero`, which can include more fields (beyond the minimally required by Google Scholar).
### Google Scholar
| Tag | YAML source | Comment |
| --- | --- | --- |
| citation_title | title | Document title |
| citation_author | author:name | Should be used for single author documents |
| citation_online_date | date | Online publication date |
| citation_fulltext_html_url | citation:URL | URL of the document |
| citation_publication_date | date | Publication date - same as online date above? |
| citation_journal_title | citation:container-title | Journal title |
| citation_reference | bibliography (parsed) | One entry per reference in bibliography |
### Zotero
Everything above plus:
| Tag | Suggested YAML source | Comment |
| --- | --- | --- |
| citation_editor | citation:editor | One entry per editor name, can be simplified to a single semicolon-separated string passed to citation_editors |
| citation_date| citation:date | Date for the citation (not necessarily when it appeared online) |
| citation_cover_date| citation:publication_date | Date of publication (date of journal issue). Used by [Springer](https://forums.zotero.org/discussion/59197/springer-useing-first-online-instead-of-real-publication-date) |
| citation_year | - | Can be automatically computed from one of the date fields |
| citation_journal_abbrev | citation:container-abbr | Correct abbreviation for the journal name |
| citation_book_title | citation:book-title | Name of the book where the paper appears |
| citation_inbook_title | citation:inbook-title | Name of the book where the paper appears |
| citation_firstpage | citation:first-page | First page number for the paper (in the journal issue) |
| citation_lastpage | citation:last-page | Last page number for the paper (in the journal issue) |
| citation_volume | citation:volume | Journal volume number |
| citation_issue | citation:issue | Journal issue number |
| citation_series_title | citation:series-title | Title of journal/book series |
| citation_publisher | citation:publisher | Name of the publisher |
| citation_doi | citation:doi | DOI, existing YAML field |
| citation_isbn | citation:isbn | ISBN |
| citation_issn | citation:issn | ISSN |
| citation_eIssn | citation:eissn | electronic ISSN |
| citation_pmid | citation:pmid | electronic PMID |
| citation_public_url | citation:public-url | URL for publicly available version, e.g. researchgame |
| citation_abstract_html_url | citation:abstract-url| URL for abstract (HTML version) |
| citation_fulltext_html_url | citation:fulltext-url | URL for full text of the paper in HTML format |
| citation_abstract | abstract | Full text of abstract, existing YAML field |
| citation_language | citation:language | Language abbreviation (EN, FR) |
| citation_conference | citation:conference | Conference name |
| citation_conference_title | citation:conference | Conference name, probably should be same as above |
| citation_dissertation_institution | citation:institution | University (for theses and dissertations) |
| citation_technical_report_institution | citation:institution | Institution (for reports), not sure we can effectively distinguish in YAML |
| citation_technical_report_number | citation:report-number | Report number |
| citation_pdf_url | citation:citation-pdf-url | URL for PDF version of the paper. Will be used by Zotero to import the paper |
| citation_keywords | keywords | Semi-colon separated keywords. Can probably be coalesced from existing YAML field |
Some of these are not consequential and can probably be delayed, while others are more important (such as `citation_doi`, `citation_isbn` and `citation_pdf_url`) and should probably be added to google-scholar partial right away.
| {
"assignee": "dragonstyle",
"comments": 8,
"created_at": "2022-07-31T13:32:19Z",
"creator": "dmi3kno",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "v1.2",
"number": 1609,
"state": "closed",
"title": "Zotero metadata for automatic parsing of citation",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1609"
} |
Following the tutorial on current MacOS, I see lots of errors.
```
>β― quarto render hello.qmd
ERROR: Jupyter kernel 'python3' not found.
```
```
β― quarto check jupyter
[β] Checking Python 3 installation....OK
Version: 3.9.9
Path: /usr/local/opt/[email protected]/bin/python3.9
Jupyter: 4.11.1
Kernels: julia-1.8
[β] Checking Jupyter engine render....OK
ERROR: Invalid jupyter YAML metadata found in file (must be string or object)
```
Most attempts to install were received with :
```
ERROR: Could not install packages due to an OSError: [Errno 13] Permission denied: '/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/bin/jsonschema'
Consider using the `--user` option or check the permissions.
```
So I think the page should contain a list of possible problems like these that might be encountered, and suggest some possible solutions. | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-31T07:25:17Z",
"creator": "cormullion",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1634,
"state": "closed",
"title": "Errors following tutorial",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1634"
} |
Many journal submissions require 1-inch margins, with a set page limit. Currently, Quarto's PDF output includes a page number at the bottom of the page, and this is included within the body text. This effectively reduces the available amount of space per page to write.
I couldn't find an existing Quarto YAML option that dealt with page numbering (like e.g. "thanks:", "linestretch:", etc.)
It would be nice if Quarto had YAML options to remove, shift position, or otherwise manipulate page numbers. I was able to fix this myself with the following YAML, but I imagine others will need this solution:
```
---
title: "Temp Title"
format:
pdf:
documentclass: scrartcl
papersize: letter
include-in-header:
text: |
\pagenumbering{gobble}
\usepackage[margin=1in]{geometry}
---
``` | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-31T00:41:17Z",
"creator": "SEthanMilne",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": null,
"number": 1606,
"state": "closed",
"title": "Feature Request: Page Number Manipulation & Options",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1606"
} |
### Bug description
The scenario is the following:
- a blog is set up with quarto template
- there is a post in a directory starting with letter "u", let's say the directory is called `posts\useful_stuff`
- the blog post is a `.qmd` file
- in a blog post, there is an `ojs` cell (doesn't matter what is inside)
- blog is rendered using `quarto render`
- blog is published to github pages using `quarto publish gh-pages`
- on a published blog on the server, when the blog post is opened, the `ojs` cells do not render any ObservableJS content, and in the console there is an Error "Uncaught SyntaxError: Invalid Unicode escape sequence"
- following the error points to the line `window._ojs.paths.runtimeToDoc = "..\..\posts\useful_stuff";` which is producing the error
- according to [this post](https://stackoverflow.com/questions/12450633/expected-hexadecimal-digit), once JS encounters a sequence "\u" in the string, it expects a unicode character, so it misreads the directory name `\useful_stuff` as a unicode string
- manually editing rendered html so that the line reads `window._ojs.paths.runtimeToDoc = "../../posts/useful_stuff";` fixes the error and the blog post gets rendered correctly
The same happens when deploying locally with the live server instead of github pages.
Please fix this bug as it will be very annoying to avoid starting the the subdirectory name with the letter "u" :)
### `quarto check` Output
_No response_
### `quarto tools check` Output
_No response_
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [ ] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [ ] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [ ] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 4,
"created_at": "2022-07-31T00:01:04Z",
"creator": "paniterka",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": null,
"number": 1605,
"state": "closed",
"title": "When publishing ojs blog posts, quarto renders the ojs runtime path with backslashes, so when a post directory starts with \"u\", OJS blocks produce Uncaught SyntaxError and the content does not render",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1605"
} |
Currently, when I set background-iframe, the site is not scrollable.
Reprex:
```
---
title: "Untitled"
format: revealjs
---
## {background-iframe="https://quarto.org"}
```
My currently workaround is
```
## {fullscreen="true"}
<iframe class="stretch" data-src="https://quarto.org/" title="https://quarto.org/">
</iframe>
```
which is basically what I want. Not sure how trivial or difficult it would be to fix, but I thought I'd note it here.
| {
"assignee": null,
"comments": 0,
"created_at": "2022-07-30T20:14:17Z",
"creator": "trangdata",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1603,
"state": "open",
"title": "Background iframe in revealjs is not scrollable",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1603"
} |
We could embed this on comments or metadata across formats. It seems like a good idea, and could help track down issues we see in the wild.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1594
<div type='discussions-op-text'>
<sup>Originally posted by **joshualeond** July 29, 2022</sup>
Is it possible to show Quarto version info somewhere inside of a rendered Quarto document? or possibly have Quarto CLI create a file with this info within my working directory?
I see that you can run `quarto --version` from the CLI and get the version but not sure if it's possible to run a Quarto specific command within a `qmd` file.
If I could show this info then I believe I could have a completely reproducible environment.
Thanks,
Josh</div> | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-30T15:38:30Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement"
],
"locked": false,
"milestone": "Future",
"number": 1601,
"state": "open",
"title": "Show Quarto version info in rendered document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1601"
} |
Ideally, we would have list of figures/tables functionality independent of format.
### Discussed in https://github.com/quarto-dev/quarto-cli/discussions/1564
<div type='discussions-op-text'>
<sup>Originally posted by **alchalu** July 28, 2022</sup>
Hello,
is there any possibility to add a list of figures or a list of tables to a word document created with Quarto?
</div> | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-30T15:13:14Z",
"creator": "cscheid",
"is_pull_request": false,
"labels": [
"enhancement",
"crossref"
],
"locked": false,
"milestone": "v1.4",
"number": 1600,
"state": "open",
"title": "Add list of figures/tables to a word document",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1600"
} |
### Bug description
Consider the minimal working example
``````
---
title: "Minimal Working Example"
format:
html:
df-print: paged
---
## Tables
```{r}
#| echo: true
#| warning: false
#| error: false
#| output: true
#| label: tbl-iris
#| tbl-cap: Edgar Anderson's Iris Data.
iris
```
``````
It produces
Now, compare with (replaced `df-print: paged` with `df-print: kable`)
``````
---
title: "Minimal Working Example"
format:
html:
df-print: kable
---
## Tables
```{r}
#| echo: true
#| warning: false
#| error: false
#| output: true
#| label: tbl-iris
#| tbl-cap: Edgar Anderson's Iris Data.
iris
```
``````
It produced
### `quarto check` Output
```
[β] Checking Quarto installation......OK
Version: 0.9.649
Path: /usr/lib/rstudio/bin/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: 4.9.2
Kernels: django_extensions, bash, python3
(|) Checking Jupyter engine render....[IPKernelApp] WARNING | Error in loading extension: django_extensions.management.notebook_extension
Check your config files in /home/raniere/.ipython/profile_default
Traceback (most recent call last):
File "/home/raniere/mambaforge/lib/python3.9/site-packages/IPython/core/shellapp.py", line 283, in init_extensions
self.shell.extension_manager.load_extension(ext)
File "/home/raniere/mambaforge/lib/python3.9/site-packages/IPython/core/extensions.py", line 76, in load_extension
return self._load_extension(module_str)
File "/home/raniere/mambaforge/lib/python3.9/site-packages/IPython/core/extensions.py", line 92, in _load_extension
mod = import_module(module_str)
File "/home/raniere/mambaforge/lib/python3.9/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 972, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 972, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 984, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'django_extensions'
Exception ignored in: <function BaseEventLoop.__del__ at 0x7fa0622399d0>
Traceback (most recent call last):
File "/home/raniere/mambaforge/lib/python3.9/asyncio/base_events.py", line 683, in __del__
self.close()
File "/home/raniere/mambaforge/lib/python3.9/asyncio/unix_events.py", line 58, in close
super().close()
File "/home/raniere/mambaforge/lib/python3.9/asyncio/selector_events.py", line 92, in close
self._close_self_pipe()
File "/home/raniere/mambaforge/lib/python3.9/asyncio/selector_events.py", line 99, in _close_self_pipe
self._remove_reader(self._ssock.fileno())
File "/home/raniere/mambaforge/lib/python3.9/asyncio/selector_events.py", line 277, in _remove_reader
key = self._selector.get_key(fd)
File "/home/raniere/mambaforge/lib/python3.9/selectors.py", line 191, in get_key
return mapping[fileobj]
File "/home/raniere/mambaforge/lib/python3.9/selectors.py", line 72, in __getitem__
fd = self._selector._fileobj_lookup(fileobj)
File "/home/raniere/mambaforge/lib/python3.9/selectors.py", line 226, in _fileobj_lookup
return _fileobj_to_fd(fileobj)
File "/home/raniere/mambaforge/lib/python3.9/selectors.py", line 42, in _fileobj_to_fd
raise ValueError("Invalid file descriptor: {}".format(fd))
ValueError: Invalid file descriptor: -1
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........OK
Version: 4.2.1
Path: /usr/lib64/R
LibPaths:
- /home/raniere/R/x86_64-pc-linux-gnu-library/4.2
- /usr/lib/R/library
rmarkdown: 2.14
[β] Checking Knitr engine render......OK
```
### `quarto tools check` Output
```
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [X] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 0,
"created_at": "2022-07-30T08:47:27Z",
"creator": "rgaiacs",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": "v1.1",
"number": 1597,
"state": "closed",
"title": "tbl-cap does not work with df-print: paged",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1597"
} |
### Bug description
Functions like `$\ket{A}$` and `$\bra{C}$` work just fine in main body, but fail in abstract when compiling to both HTML and PDF.
The if one deletes the end quote and uncomments the end of line 13 below (the abstract), the build fails, error given is " ERROR: YAMLError: unknown escape sequence at line 13, column 32:
abstract: "We test `$1+1$` and `$\ket{j}$`." "
I just installed Quarto on Mac Ventura and using VSCode with the Quarto extension v1.29.0.
Example .qmd file:
```
---
title: "Testing, testing 1,2"
author:
name: "Auhor Name"
affiliation: "Places"
date: "07/29/2022"
format:
html:
code-fold: true
pdf:
include-in-header:
text: \usepackage{physics}
abstract: "We test $1+1$ and $\ket{j}$." uncomment that bit to test
---
$\ket{j}$ works here as does $\bra{H}$.
```
### `quarto check` Output
```zsh
% quarto check
[β] Checking Quarto installation......OK
Version: 1.0.37
Path: /Applications/quarto/bin
[β] Checking basic markdown render....OK
[β] Checking Python 3 installation....OK
Version: 3.8.5 (Conda)
Path: /Users/joshjob42/opt/anaconda3/bin/python
Jupyter: 4.6.3
Kernels: julia-1.6, julia-1.8, julia-1.7, python3
[β] Checking Jupyter engine render....OK
[β] Checking R installation...........(None)
Unable to locate an installed version of R.
Install R from https://cloud.r-project.org/
```
### `quarto tools check` Output
```zsh
% quarto tools check
[β] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
```
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [x] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [X] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [X] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": null,
"comments": 1,
"created_at": "2022-07-30T04:54:37Z",
"creator": "joshjob42",
"is_pull_request": false,
"labels": [
"bug"
],
"locked": false,
"milestone": null,
"number": 1595,
"state": "closed",
"title": "Commands like $\\ket{A}$ work in main body but not in abstract",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1595"
} |
Currently some option cannot be found in search like `class-output` only available for knitr chunks.
Those should be added, possibly with lower weight than main guide page results. | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-30T00:21:44Z",
"creator": "cderv",
"is_pull_request": false,
"labels": [
"documentation"
],
"locked": false,
"milestone": null,
"number": 1592,
"state": "closed",
"title": "Add knitr and jupyter cells option in search ",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1592"
} |
### Bug description
When using ojs_define with Python and pandas, it is not possible to pass an instance of pd.Series, while it is possible to do so for a pd.Dataframe. If a series is passed, ojs_define produces a type error and stops the render:
`TypeError: Object of type Series is not JSON serializable`
In order for ojs_define to work, the series need to be converted to dataframes first which is cumbersome (series get used really often). For a better pandas-ojs integration it would be beneficial to include pd.Series support in ojs_define such as it is done for pd.Dataframe, or at least to produce a more meanigful error description, pointing to the need to convert to a dataframe.
Minimal working example:
````
---
title: "ojs_define"
format: html
jupyter: python3
---
```{python}
import pandas as pd
my_variable = pd.Series([0,1,2,3])
# ojs_define(my_variable = pd.DataFrame(my_variable)) # this works
ojs_define(my_variable = my_variable) # this doesn't
```
```{ojs}
my_variable
```
````
### `quarto check` Output
[>] Checking Quarto installation......OK
Version: 1.0.37
Path: C:\Users\tkubacka\AppData\Local\Programs\Quarto\bin\
CodePage: 1252
[>] Checking basic markdown render....OK
[>] Checking Python 3 installation....OK
Version: 3.8.10 (Conda)
Path: C:/APPS/Anaconda3/python.exe
Jupyter: 4.10.0
Kernels: python3, dashenv
[>] Checking Jupyter engine render....OK
[>] Checking R installation...........OK
Version: 4.1.2
Path: C:/Users/tkubacka/Documents/R/R-4.1.2
LibPaths:
- C:/Users/tkubacka/Documents/R/R-4.1.2/library
rmarkdown: 2.11
[>] Checking Knitr engine render......OK
### `quarto tools check` Output
[>] Inspecting tools
Tool Status Installed Latest
chromium Not installed --- 869685
tinytex Not installed --- v2022.07
### Checklist
- [X] [formatted your issue](https://yihui.org/issue/#please-format-your-issue-correctly) so it is easier for us to read?
- [X] included a minimal, fully reproducible example in a single .qmd file? Please provide the whole file rather than the snippet you believe is causing the issue.
- [X] documented the quarto version you're running, by pasting the output from running `quarto check` in the "Quarto Check Output" text area?
- [X] documented the version of the quarto tools you're running, by providing the output from running `quarto tools check` in the "Quarto Tools Check Output" text area?
- [ ] documented the RStudio IDE version you're running (if applicable), by providing the value displayed in the "About RStudio" main menu dialog?
- [ ] documented which operating system you're running? If on Linux, please provide the specific distribution as well.
- [ ] upgraded to the latest version, including your versions of R, the RStudio IDE, and relevant R packages? | {
"assignee": "cscheid",
"comments": 1,
"created_at": "2022-07-29T23:18:31Z",
"creator": "paniterka",
"is_pull_request": false,
"labels": [
"bug",
"ojs-engine"
],
"locked": false,
"milestone": "Future",
"number": 1589,
"state": "closed",
"title": "In Python, ojs_define() fails when trying to pass pd.Series",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1589"
} |
I've started to write all of my personal notes in Quarto, and as I use the Zettelkasten method, what would be really great would be to have some kind of two-way links between pages. One way to do this would be to have an option to have some kind of 'what links here' section at the bottom of each page to make links more bidirectional.
Thank you for the amazing project! | {
"assignee": null,
"comments": 2,
"created_at": "2022-07-29T19:58:27Z",
"creator": "supertrianguloid",
"is_pull_request": false,
"labels": [],
"locked": false,
"milestone": "Future",
"number": 1585,
"state": "open",
"title": "Backlinks in website output",
"url": "https://github.com/quarto-dev/quarto-cli/issues/1585"
} |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.