module code checks report possible issues

[achubaty]

missing or incorrect metadata

• Biomass_borealDataPrep: defineParameter: 'speciesUpdateFunction' is not of specified type 'list'.
• Biomass_borealDataPrep: outputObjects: standAgeMap, rstLCC, firePerimeters, speciesLayers, studyAreaLarge, cloudFolderID, ecoregionGroup are assigned to sim inside createBiomass_coreInputs, but are not declared in metadata outputObjects
• Biomass_borealDataPrep: inputObjects: imputedPixID is assigned to sim inside .inputObjects, but is not declared in metadata inputObjects
• Biomass_borealDataPrep: inputObjects: sppColorsVect, longevity, ecoregionGroup, pixelGroup are used from sim inside createBiomass_coreInputs, but are not declared in metadata inputObjects

declared in metadata but not used/created

• Biomass_borealDataPrep: module code: rawBiomassMap is declared in metadata outputObjects, but is not assigned in the module

function name conflicts

• Biomass_borealDataPrep: module code: the following function(s) is used that conflict(s)
  with base functions: scale, scale
  It is a good idea to be explicit about the package sources, e.g., raster::scale but only for the 'get' functions, not the 'set' function
  (e.g., don't change when on the left hand side of an assignment operator)

no default inputs provided

(probably OK)

• Biomass_borealDataPrep: module code: cloudFolderID, ecoregionRst are declared in metadata inputObjects, but no default(s) are provided in .inputObjects

unused local variables

(very likely OK)

• Biomass_borealDataPrep: module code: createBiomass_coreInputs: local variable ‘out’ assigned but may not be used (Biomass_borealDataPrep.R:801)
• Biomass_borealDataPrep: module code: createBiomass_coreInputs: local variable ‘timePriorToFit’ assigned but may not be used (Biomass_borealDataPrep.R:848)
• Biomass_borealDataPrep: module code: plotFn_speciesEcoregion: local variable ‘ggSpeciesEcoregion’ assigned but may not be used (R/plotFn_speciesEcoregion.R:2-9)
• Biomass_borealDataPrep: module code: spinUpPartial: local variable ‘mySimOut’ assigned but may not be used (R/updateYoungBiomasses.R:194-202)
• Biomass_borealDataPrep: module code: spinUpPartial: local variable ‘opts’ assigned but may not be used (R/updateYoungBiomasses.R:157-162)
• Biomass_borealDataPrep: module code: updateYoungBiomasses: local variable ‘PI.time’ assigned but may not be used (R/updateYoungBiomasses.R:35-40)

[achubaty]

@CeresBarros some of these are real issues nthat need to be addressed ASAP -- maybe bad merges?

[CeresBarros]

I'll have a look, but some have an answer:
(in resync-devel branch)

Biomass_borealDataPrep: defineParameter: 'speciesUpdateFunction' is not of specified type 'list'.

I see the default being list(quote(LandR::speciesTableUpdate(sim$species, sim$speciesTable, sim$sppEquiv, P(sim)$sppEquivCol))) and:

> is(list(quote(LandR::speciesTableUpdate(sim$species, sim$speciesTable, sim$sppEquiv, P(sim)$sppEquivCol))), 'list')
[1] TRUE

So not sure why this is being flagged. Could you be overriding defaults?

Biomass_borealDataPrep: inputObjects: sppColorsVect, longevity, ecoregionGroup, pixelGroup are used from sim inside createBiomass_coreInputs, but are not declared in metadata inputObjects

I see sppColorsVect missing from the metadata indeed. the others I don't see being used from sim and they are column names

Biomass_borealDataPrep: module code: rawBiomassMap is declared in metadata outputObjects, but is not assigned in the module

I see rawBiomassMap being assigned to sim in .inputObjects

Biomass_borealDataPrep: module code: cloudFolderID, ecoregionRst are declared in metadata inputObjects, but no default(s) are provided in .inputObjects

both are optional -- so more a problem of bad documentation here

[CeresBarros]

I can fix many of these , but where do I push to?