Interactive vignette

[maelle]

👋 @phuongquan! On R-universe, until you upped the package version, building this vignette

mantis/vignettes/articles/example-report-interactive.Rmd

Line 14 in 37775ca

# only generate it if this is a release version

failed with the following message:

Error: 
! in callr subprocess.
Caused by error in `.f(.x[[i]], ...)`:
! Failed to render vignettes/articles/example-report-interactive.Rmd.
✖ Quitting from example-report-interactive.Rmd:13-40 [generate-report]
Caused by error:
! Invalid argument(s) supplied.
file: Expected a single path to an existing directory, filename should only contain alphanumeric, '-', and '_' characters, and include extension '.html': Found [ class = character; contents = ../../docs/articles/example-prescriptions-interactive.html].
---

Does that ring any bell?

For the record, even after downgrading the version number manually, locally I am able to build the pkgdown website.

Cc @jeroen

[phuongquan]

Hi @maelle, I'm not sure I understand what the problem is.

That vignette is used to create the example interactive report in the pkgdown website and as far as I can see it has been created successfully in the various live locations:
https://ropensci.github.io/mantis/articles/example-report-interactive.html
https://ropensci.github.io/mantis/dev/articles/example-report-interactive.html
https://docs.ropensci.org/mantis/articles/example-report-interactive.html

and the website builds successfully when I build it locally too (with release and dev version numbers).

The error you quoted was possibly caused by the relative path ../../docs/articles/ not existing wherever it was trying to be built from?

[jeroen]

The error you quoted was possibly caused by the relative path ../../docs/articles/ not existing wherever it was trying to be built from?

Is this supposed to be the current build directory? We build to another destination directory that is not called docs, so you should not hardcode that. Where does this file example-prescriptions-interactive.html that you are trying to acces come from? I don't see any source file with such a name?

[phuongquan]

The vignette vignettes/articles/example-report-interactive.Rmd generates the example-prescriptions-interactive.html file (only if it is a release version):

mantis/vignettes/articles/example-report-interactive.Rmd

Lines 14 to 39 in 37775ca

	# only generate it if this is a release version
	if (
	length(unlist(strsplit(
	as.character(utils::packageVersion("mantis")),
	"[.]"
	))) <
	4
	) {
	example_prescription_numbers <- mantis::example_prescription_numbers
	filename <-
	mantis::mantis_report(
	df = example_prescription_numbers,
	file = "../../docs/articles/example-prescriptions-interactive.html",
	inputspec = mantis::inputspec(
	timepoint_col = "PrescriptionDate",
	item_cols = c("Antibiotic", "Spectrum", "Location"),
	value_col = "NumberOfPrescriptions",
	tab_col = "Location"
	),
	outputspec = mantis::outputspec_interactive(),
	report_title = "Example mantis report - interactive",
	dataset_description = "Hover mouse over the graphs to see dates and values. Filter the table by typing into the boxes under the column headings.",
	show_progress = FALSE
	)
	}

It generates the html file in a location in the pkgdown site where it expects to be able to find it again, (i.e. in the ../../docs/articles/ relative folder when built locally or in github pages):

mantis/vignettes/articles/example-report-interactive.Rmd

Line 27 in 37775ca

file = "../../docs/articles/example-prescriptions-interactive.html",

This is so that the same vignette can then display the generated html file within an iframe:

mantis/vignettes/articles/example-report-interactive.Rmd

Lines 48 to 50 in 37775ca

	```{=html}
	<iframe src="https://ropensci.github.io/mantis/articles/example-prescriptions-interactive.html" width="100%" height="900">
	</iframe>

Does that make sense?

If R-universe builds the site at a different location, how can I find what that destination is dynamically? Or else instruct it not to build the example report?