Package checks

[diazrenata]

• [ ] R CMD Check
• [ ] CI tests
• [ ] CI test coverage

[ajrominger]

Clean up documentation so the only things exported are what we really want exported. This means:

• only very intentionally exporting rcpp things (default should be nothing exported)
• figure out what sp1_gr is and why it's exported
• figure out why exportPattern("^[[:alpha:]]+") is in namespace
• figure out do $ and [ need to be in exports if what we're doing is defining new methods for these generics

We also need to make sure all arguments are documented in ./man/ files

[diazrenata]

Outstanding warnings:

• [ ] data contains no datasets --> remove data
• [ ] numerous undocumented code objects --> add docs, this will be tedious but straightforward
• [ ] contents of data directory --> could use inst
• [ ] rlang imports in tests --> currently just commenting out problematic tests, will want to sleuth more here later

[ajrominger]

@diazrenata it seems like a lot of the undocumented things boil down to just an issue with file order. for example, documenting getFinalState gives a warning that roleModel and roleExperiment are undefined. but they are defined, it's just that they're defined in a file that alphabetically comes after the file where getFinalState is defined. the solution (short of renaming the files) is to use the @include roxygen tag.

so, for example, the file defining getFinalState will need to include this in the roxygen "preamble":

#' @include roleModel.R roleExperiment.R

[diazrenata]

Yep, that’s a lot of them!

On May 5, 2023, at 12:19 PM, Andy Rominger @.***> wrote:

@diazrenata https://github.com/diazrenata it seems like a lot of the undocumented things boil down to just an issue with file order. for example, documenting getFinalState gives a warning that roleModel and roleExperiment are undefined. but they are defined, it's just that they're defined in a file that alphabetically comes after the file where getFinalState is defined. the solution (short of renaming the files) is to use the @include roxygen tag.

so, for example, the file defining getFinalState will need to include this in the roxygen "preamble":

' @include roleModel.R roleExperiment.R

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[ajrominger]

connected to #60, #97, #111, #112 and #122