ecohealthalliance / targets-mermaid-test

Test for Target Version and Mermaid Rendering Issues

Reproducible Example of Test for Target Version and Mermaid Rendering Issues

Problem

A mermaid graph embedded in an Rmarkdown document that is rendered via a targets workflow is erroring with the following message:

argument "store" is missing, with no default

This document used to render properly without issues at earlier stages of project but after a few months and a few targets versions later (started at v1.1.3 and currently at v1.3.2), the error above was encountered.

Hence the suspicion that maybe targets version was the culprit more so that there is discussion online that the initial version of targets that introduces the tar_mermaid() functionality has had some major bugs with regard to mermaid graph rendering within Rmarkdown documents.

Test

We recreated a targets workflow in the repository using example created by Will Landau here which is also an example in the function documentation for tar_mermaid().

We added a target for rendering an Rmarkdown report found inside a specific library called reports which mimics the structure of the project in which the issue/problem was occurring.

To be able to control the version of targets used, this repository uses renv.

We first installed targets version 1.3.2:

renv::install("targets@1.3.2")

and then ran the workflow with targets::tar_make()

This reproduced the same error we were encountering in existing project.

Then, we installed targets version 1.4.1:

renv::install("targets@1.4.1")

and then ran the workflow.

Workflow completed without errors and HTML output in reports directory was produced as expected.

Finally, we tested using targets version 1.1.3 which is the version used at the start of the project. After installing this version and running the workflow, we completed the and rendered the document without errors/issues.