tar_quarto() returns Error : ! System command 'quarto' failed

[turbanisch]

I am trying to include a Quarto website project as a target but keep getting the error Error : ! System command 'quarto' failed. I am working in an R Studio Project (which is where the targets pipeline is defined) and the homepage files are another R Studio Project in a subfolder called homepage. For now, the homepage files do not invoke any other targets.

Edit: It turned out that the culprit was a file path I used to embed an image with

knitr::include_graphics("img/my_image.jpg")

Adding homepage/ to the path (i.e. making it relative to the top-level project in which the targets pipeline lives) made it work. Perhaps a comment in the targets user manual would be useful? It would also be great if the error message could be more specific but I see that this might be hard to implement.

For my case, it is probably best practice to define a new target for the image file rather than hard-coding it anyways.

[wlandau]

A tar_quarto() target calls quarto::quarto_render(), so it is best to test with the latter first. As for error messages, the Quarto stack currently does not forward them up, so it depends on quarto-dev/quarto-r#16.

[turbanisch]

Thank you so much! I followed your suggestion and tried rendering the files both with tar_make() and quarto::quarto_render("homepage/"). With the latter, all file paths seem to be based on homepage/ as root. With tar_make(), I have to add homepage/ to the file paths when reading in files.

I now encounter a problem that has probably to do with the object type: I can load and embed a figure (created as a ggplot2 object) with both render commands using

readr::read_rds("homepage/import/figure.rds")

but loading and embedding a table (created as a gt table object) the same way only works with quarto::quarto_render("homepage/"). With tar_make() I get the error message from above.

Given that the error seems to depend on object type, could it have to do with the packages targets is loading in the background? I do include the gt package in tar_options_set(). It also works in a dummy document that I knit without targets (via point-and-click in R Studio):

---
title: Test
output: html
---

```{r}
readr::read_rds("homepage/import/table.rds")
```

It also works when I replace the gt table object with a simple dataframe.

[wlandau]

Thank you so much! I followed your suggestion and tried rendering the files both with tar_make() and quarto::quarto_render("homepage/"). With the latter, all file paths seem to be based on homepage/ as root. With tar_make(), I have to add homepage/ to the file paths when reading in files.

The pipeline needs to each target from the project root (execute_dir = getwd() in quarto_render()) to ensure the report can load any dependent targets from the _targets/ data store.

I now encounter a problem that has probably to do with the object type: I can load and embed a figure (created as a ggplot2 object) with both render commands using

Some objects like gt tables need the package loaded to render. You could call library(gt) in a code chunk for that.

[turbanisch]

Thanks again! Calling library(gt) in the chunk doesn't seem to help though.
I created a minimal example here: https://github.com/turbanisch/quarto-target-test The pipeline only creates a single gt-formatted table object which is then embedded in index.qmd in the homepage folder. If I run the code as it is, the table object is printed as a list. When I add library(gt), I get the error Error : ! System command 'quarto' failed again. Adding the chunk option #| results: asis doesn't seem to help either (and isn't generally necessary when embedding gt objects in RMarkdown/Quarto documents).
Sorry for taking so much of your time - hopefully this isn't just something that is not working on my machine.

[wlandau]

I looked back, and it is caused by an issue in gt:

• gtsummary stopped working with targets when Rmd not placed in main folder targets#920 (comment)
• fails if doc is in a subdirectory rstudio/gt#1040
• fix for gt/Rmd in subdir #1040 , change as suggested in ropensci/targets#920 (comment) rstudio/gt#1063
• correctly detect the docx output format for pandoc conversion rstudio/gt#1084
• Rstudio: Quarto file within a subdirectory and gt tables not rendering quarto-dev/quarto-cli#2996

A solution could be to upgrade the Quarto CLI or downgrade gt to 0.6.0.

[turbanisch]

Updating Quarto CLI solved it! Thanks for all the time you put into this, I truly appreciate it. Not sure I would have been able to figure this out by myself at all (I switched to knitr::kable() in the meantime).

[turbanisch]

I have another question that is likely related: When I try to embed an image into the Quarto document (via knitr::include_graphics("homepage/img/Rplot.png")), the pipeline throws an error if I define the image path relative to the qmd document (i.e., without "homepage/" in the path). When I define it relative to the project (where the pipeline lives) as above, the pipeline runs without error but the image path is broken:

Apparently the image path in the resulting html file is not adapted (<p><img src="homepage/img/Rplot.png" class="img-fluid"></p>). Do you know of a way to fix this? I can't think of another way to define the relative file path. I put the example here: https://github.com/turbanisch/quarto-target-test
I would also be interested in a solution that tracks the file path as a target and embeds it via tar_read() but in my experiments the same issue occured.

[wlandau]

It's the same issue: targets needs to render the site with execute_dir at the project root, but the figures are referenced using relative paths. Regular Markdown syntax ![](./img/Rplot.png) and withr::with_dir("homepage", knitr::include_graphics("./img/Rplot.png")) both seem to work.

I would also be interested in a solution that tracks the file path as a target and embeds it via tar_read() but in my experiments the same issue occured.

Something like withr::with_dir("homepage", knitr::include_graphics(tar_read(image_file))) would probably do it.

[turbanisch]

Thanks again! It works fine without tar_read() now but I can't get it to work with the last approach you suggested. Probably it's fine just embedding the image files outside the pipeline but I was trying to understand the mechanics of it. Since tar_read(image_file) already returns a file path that starts with "homepage/" I was wondering if we would not have to remove this part in order to make it relative to the homepage directory (or move up with ..)?

[wlandau]

Yeah, either you would need to remove the "homepage" part or call tar_read(image_file) separately from ![](./img/Rplot.png) (declaring the dependency and embedding the image in different lines).