I am building Wave containers for a workflow, and have hit a Bioconductor package requirement which is called by a package I included but not listed in its Depends or Imports, only in the Suggests. (I disagree about whether this is the correct choice but 🤷‍♀️) The developer suggests "you can install it automatically by adding 'dependencies = TRUE' to your install command" which assumes I am using BiocManager::install directly, rather than coming from Wave through the bioconda recipe. The actual questions: Is there a generic way to include all Suggests packages? Is this a terrible idea? Should I just treat this as a special case, include the dependency in my list, and hope this isn't an issue that comes up often?

I would say include the dependency.

It sounds like an odd choice for the listing and I'd treat it as a one-off. With that said, I don't think anything should necessarily break by always including suggests/all dependencies (but you'd probably run into errors more often due to simple package rot).