Misleading/wrong module code checks

[CeresBarros]

SpaDES,core module code checks are warning about non-declared (in metadata) inputs which are actually temporary objects using during the simulation.
In the message below, r, nn and sppKeep are not in sim.

Biomass_speciesData: inputObjects: r, nn, sppKeep are used from sim inside biomassDataInit, but are not declared in metadata inputObjects

reprex (currently failing downstream from the code checks, tho see PredictiveEcology/SpaDES.project#40)

Require::Require("PredictiveEcology/SpaDES.project@windowsTesting")
inputPath <- "D:/GitHub/LandR-tutorials/LandRDemo_coreVeg/inputs"

## it seems `params =`is evaluated first so all of these need to be defined here.
sppEquivCol <- "Boreal"
vegLeadingProportion <- 0
successionTimestep <- 10L
eventCaching <- c(".inputObjects", "init")
useParallel <- FALSE
simTimes <- list(start = 2001, end = 2031)

out <- setupProject(name = "LandRDemo_coreVeg",
                    options = list(
                      "reproducible.destinationPath" = inputPath
                      , "reproducible.useCache" = TRUE
                      , "reproducible.useNewDigestAlgorithm" = 2
                      , "reproducible.useTerra" = TRUE
                      , "spades.moduleCodeChecks" = TRUE
                      , "spades.inputPath" = inputPath
                    ),
                    paths = list(
                      projectPath = "D:/GitHub/LandR-tutorials/LandRDemo_coreVeg"
                      , modulePath = "D:/GitHub/LandR-tutorials/LandRDemo_coreVeg/modules"
                      , inputPath = inputPath
                      , scratchPath = tempdir()
                      , packagePath = "D:/GitHub/LandR-tutorials/packages"
                    ),
                    modules = c(
                      "PredictiveEcology/Biomass_speciesData@terra-migration"
                      , "PredictiveEcology/Biomass_borealDataPrep@terra-migration"
                      , "PredictiveEcology/Biomass_speciesParameters@development"
                      , "PredictiveEcology/Biomass_core@terra-migration"
                      , "PredictiveEcology/Biomass_validationKNN@development"
                    ),
                    ##
                    ## NECESSARY OBJECTS -----------------------------------
                    ## STUDY AREA(S)
                    studyAreaLarge = {
                      originalcrs <- "+proj=longlat +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0"
                      Biomass_corecrs <- "+proj=lcc +lat_1=49 +lat_2=77 +lat_0=0 +lon_0=-95 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"

                      largeExtent <- c(xmin = -104.757, xmax = -104.2197, ymin = 55.68663, ymax = 56.20319)
                      studyAreaL <- terra::vect(terra::ext(largeExtent))
                      studyAreaL <-  terra::vect(terra::geom(studyAreaL), "polygons", crs = originalcrs, atts = data.frame(id = 1:length(studyAreaL)))
                      studyAreaL <- terra::project(studyAreaL, Biomass_corecrs)
                      studyAreaL
                    },
                    studyArea = {
                      originalcrs <- "+proj=longlat +datum=NAD83 +no_defs +ellps=GRS80 +towgs84=0,0,0"
                      Biomass_corecrs <- "+proj=lcc +lat_1=49 +lat_2=77 +lat_0=0 +lon_0=-95 +x_0=0 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80 +towgs84=0,0,0"

                      smallExtent <- c(xmin = -104.757, xmax = -104.48835, ymin = 55.68663, ymax = 55.94491)
                      studyAreaS <- terra::vect(terra::ext(smallExtent))
                      studyAreaS <-  terra::vect(terra::geom(studyAreaS), "polygons", crs = originalcrs, atts = data.frame(id = 1:length(studyAreaS)))
                      studyAreaS <- terra::project(studyAreaS, Biomass_corecrs)
                      studyAreaS
                    },
                    ##
                    ## SPECIES LISTS
                    sppEquiv = {
                      data("sppEquivalencies_CA", package = "LandR")
                      sppEquivalencies_CA[grep("Pin", LandR), `:=`(EN_generic_short = "Pine",
                                                                   EN_generic_full = "Pine",
                                                                   Leading = "Pine leading")]
                      sppEquivalencies_CA[grep("Betu_pap", LandR), `:=`(EN_generic_short = "Birch",
                                                                        EN_generic_full = "Birch",
                                                                        Leading = "Birch leading")]
                      ## all Popu will be merged
                      sppEquivalencies_CA[grep("Popu_", LandR), `:=`(EN_generic_short = "Poplar",
                                                                     EN_generic_full = "Poplar",
                                                                     Leading = "Poplar leading")]
                      sppEquivalencies_CA[grep("Popu_", LandR), Boreal := "Popu_Spp"]

                      ## define spp column to use for model
                      # sppEquivCol <- "Boreal"
                      sppEquivalencies_CA <- sppEquivalencies_CA[!"", on = sppEquivCol]
                      sppEquivalencies_CA <- na.omit(sppEquivalencies_CA, sppEquivCol)
                      sppEquivalencies_CA
                    },
                    sppColorVect = {
                      LandR::sppColors(sppEquiv, sppEquivCol, newVals = "Mixed", palette = "Accent")
                    },
                    speciesParams = {
                      list(
                        "shadetolerance" = list(
                          Betu_Pap = 1
                          , Lari_Lar = 1
                          , Pice_Gla = 2
                          , Pice_Mar = 3
                          , Pinu_Ban = 1.5
                          , Popu_Spp = 1
                        )
                      )
                    },
                    ##
                    ## SIMULATION SETUP ------------------------------------
                    times = simTimes,
                    params = source("params.R")
)

simInitOut <- do.call(SpaDES.core::simInit, out)

[CeresBarros]

Found another one in the same example

rawBiomassMap is being assigned to sim in .inputObjects, but the following warning is issued:

D:/GitHub/LandR-tutorials/LandRDemo_coreVeg/modules/Biomass_borealDataPrep/Biomass_borealDataPrep.R
Biomass_borealDataPrep: module code: rawBiomassMap is declared in metadata outputObjects, but is not assigned in the module

[achubaty]

with #223