build is failing because of missing documentation

[ajrominger]

this is the error report:

  Undocumented code objects:
    ‘buildFun’ ‘cFun’ ‘checkRolePhylo’ ‘dataFunCpp’ ‘getFinalState’
    ‘getSumStats’ ‘getSumStatsMean’ ‘getValuesFromParams’ ‘hillAbund’
    ‘hillGenetic’ ‘hillPhylo’ ‘hillTrait’ ‘intFunCpp’ ‘iterModelCpp’
    ‘localComm’ ‘metaComm’ ‘rawAbundance’ ‘rawApePhylo’
    ‘rawBranchLengths’ ‘rawGenDiv’ ‘rawSeqs’ ‘rawSpAbundance’ ‘rawSppID’
    ‘rawTraits’ ‘richness’ ‘roleData’ ‘roleDataFromCpp’ ‘roleDataToCpp’
    ‘roleExperiment’ ‘roleModel’ ‘roleParams’ ‘runRole’ ‘setContext’
    ‘sim_seqs’ ‘testRand’ ‘untbParams’ ‘vectFunCpp’ ‘writeRole’
  Undocumented S4 classes:
    ‘roleModel’ ‘roleParams’ ‘metaComm’ ‘roleExperiment’ ‘localComm’
    ‘roleData’
  Undocumented S4 methods:
    generic '[' and siglist 'roleExperiment,ANY,ANY,ANY'
    generic '$' and siglist 'roleExperiment'
    generic 'getFinalState' and siglist 'roleExperiment'
    generic 'getFinalState' and siglist 'roleModel'
    generic 'getSumStats' and siglist 'roleData'
    generic 'getSumStats' and siglist 'roleExperiment'
    generic 'getSumStats' and siglist 'roleModel'
    generic 'hillAbund' and siglist 'roleData'
    generic 'hillGenetic' and siglist 'roleData'
    generic 'hillPhylo' and siglist 'roleData'
    generic 'hillTrait' and siglist 'roleData'
    generic 'rawAbundance' and siglist 'roleData'
    generic 'rawApePhylo' and siglist 'roleData'
    generic 'rawBranchLengths' and siglist 'roleData'
    generic 'rawGenDiv' and siglist 'roleData'
    generic 'rawSeqs' and siglist 'roleData'
    generic 'rawSpAbundance' and siglist 'roleData'
    generic 'rawSppID' and siglist 'roleData'
    generic 'rawTraits' and siglist 'roleData'
    generic 'richness' and siglist 'roleData'
    generic 'runRole' and siglist 'roleExperiment'
    generic 'runRole' and siglist 'roleModel'
    generic 'setContext' and siglist 'roleExperiment'
    generic 'writeRole' and siglist 'roleExperiment'

a few are functions we don't want (e.g. cfun), many are things we in fact don't want to be exported (like checkRolePhylo) and a lot are simply things we need to document.

the things we don't want to be exported are getting exported because we have #' @exportPattern "^[[:alpha:]]+" in the roleR-package.R file. I'm not sure why we have that there, we should see if we can remove it without breaking everything

[diazrenata]

Is this the build on GitHub Actions or also the build on your machine?

I had a few work sessions a couple of weeks ago where I got these errors resolved locally, but they continue to fail on Actions. At that point I let it go for the time being because I realized we didn't need these to pass in order to get Runiverse to build binaries. When it's time to get actions to pass (and it may be that time!) I can revisit. It'll be a debug in the actions docs rendering, I think.

[ajrominger]

oh yeah thanks for this clarification: the build issue is with GitHub Actions