Creating self-contained reports from pkg/inst/

[llrs-roche]

Description

I am currently working to make reports of packages for the R Regulatory repository. To provide some example and provide some guidance on key aspects of how the reports can be generated we created a package at https://github.com/pharmar/riskreports

These reports are not meant (for the moment) to be modified by the user, but only run automatically in a validated image (docker or some similar technology) with a set of software and R packages to report information about a single R package. As such we use parametrized reports and not a template, in addition, as is meant to be generated in a virtual machine or other systems we are not using quarto projects.

The package provides a quarto document and a function to render it on several formats (HTML or gfm for web rendernig. We will also implement a PDF version of the report) using quarto::quarto_render. I'm filling this discussion to show my poor attempts to get this working, as indicated on #5765 (comment) . My attempts were made without quarto cli, but I think they are not related to quarto-r:

Working on the fix_workaround branch and running:

package_report(
  package_name = "dplyr",
  package_version = "1.1.4",
  params = list(
    assessment_path = "inst/assessments/dplyr.rds",
    image = "rhub/ref-image")
 ) 

I see the following error (with quarto 1.7.13):

ERROR: NotFound: The system cannot find the path specified. (os error 3): readfile 'pkg_template_files\libs\quarto-html\quarto.js'
Path: pkg_template_files\libs\quarto-html\quarto.js

Note the key call using output_file:

out <- quarto::quarto_render(
        template_path,
        output_format = "all",
        execute_params = params,
        output_file = paste0("validation_report_", full_name),
        ...
      )

[mcanouil]

Be sure to delete assets in _freeze directory.

[llrs-roche]

There is no _freeze directory on the package root directory or on the inst/report/. But there is one inst\report\pkg_template_files, should I delete that instead?

[mcanouil]

In 1.7.* pre-releases, there were some changes/refactoring in quarto.js this lead to improvements but also few dependency/import issues that should be resolved.

I did not look at your code to see what you do with output (directory and files), etc.

The best would be to cleanup any previous computations/rendering and make a clean render using the latest pre-release.

FYI, when changing output files/directory:

• Output directory in quarto-cli #2171
• Rendering a document in subfolder with -o flag leads to libs not found #5765

I summarised various combinations leading to different behaviours which might be at play.
https://github.com/mcanouil/quarto-issues-experiments/tree/main/quarto-cli-2171#readme

Note that if you output to a directory outside your project (defined by _quarto.yml or location of your single document), the output directory is no longer cleaned up.

quarto render --outpdur-dir ../whatever # -> no clean up of `../whatever` content

quarto render --outpdur-dir whatever # -> `whatever` content is removed

[llrs-roche]

Many thanks for your help, the linked resources helped me specially this comment: quarto-dev/quarto-r#81 (comment). Apologies for the not carefully checking everything before.