Biomass_core spin-up replaces Biomass_borealDataPrep's init event entry in completed

[CeresBarros]

after running the spin-up, Biomass_borealDataPrep's init event no longer appears in the completed events list:

> completed(preSimListbaseCase)
   eventTime                moduleName          eventType eventPriority           clockTime
1:      2001                checkpoint               init             0 2022-03-22 17:20:39
2:      2001                      save               init             0 2022-03-22 17:20:39
3:      2001                  progress               init             0 2022-03-22 17:20:39
4:      2001                      load               init             0 2022-03-22 17:20:39
5:        38              Biomass_core mortalityAndGrowth             6 2022-03-22 17:25:27
6:      2001 Biomass_speciesParameters               init             1 2022-03-22 17:25:52
7:      2001              Biomass_core               init             1 2022-03-22 17:25:52

> modules(preSimListbaseCase)
$`D:/GitHub/LandRBiomass_publication/R/SpaDES/m/Biomass_borealDataPrep`
[1] "Biomass_borealDataPrep"

$`D:/GitHub/LandRBiomass_publication/R/SpaDES/m/Biomass_speciesParameters`
[1] "Biomass_speciesParameters"

$`D:/GitHub/LandRBiomass_publication/R/SpaDES/m/Biomass_core`
[1] "Biomass_core"

> ls(preSimListbaseCase)
 [1] "activePixelIndex"                 "activePixelIndexReporting"        "biomassMap"                       "cloudFolderID"
 [5] "cohortData"                       "columnsForPixelGroups"            "ecoregion"                        "ecoregionLayer"
 [9] "ecoregionMap"                     "factorialSpeciesTable"            "imputedPixID"                     "inactivePixelIndex"
[13] "inactivePixelIndexReporting"      "lastFireYear"                     "lastReg"                          "minRelativeB"
[17] "modelBiomass"                     "modelCover"                       "nonZeroCover"                     "numTreed"
[21] "pixelFateDT"                      "pixelGroupMap"                    "PSPgis"                           "PSPmeasure"
[25] "PSPplot"                          "rasterToMatch"                    "rasterToMatchLarge"               "rawBiomassMap"
[29] "reducedFactorialCohortData"       "rstLCC"                           "simulationOutput"                 "species"
[33] "speciesEcoregion"                 "speciesGAMMs"                     "speciesLayers"                    "speciesParams"
[37] "speciesTable"                     "sppColorVect"                     "sppEquiv"                         "standAgeMap"
[41] "studyArea"                        "studyAreaLarge"                   "studyAreaReporting"               "sufficientLight"
[45] "treed"                            "treedFirePixelTableSinceLastDisp" "vegTypeMap"

I am sure Biomass_borealDataPrep finished running because all it's outputs are there and the whole simulation worked fine

Maybe related, is the fact that I also now get a warning after running elapsedTime on the output simList of a spades call on the previously initialised simulation:

> elapsedTime(simListbaseCase$sim1_rep01)
                   moduleName                 eventType       elapsedTime
 1:                checkpoint                      init 1.994133e-03 secs
 2:                      save                      init 2.991915e-03 secs
 3:                  progress                      init 9.980202e-04 secs
 4:                      load                      init 2.887025e+02 secs
 5:              Biomass_core        mortalityAndGrowth 2.692351e+01 secs
 6: Biomass_speciesParameters                      init 2.055149e-01 secs
 7:              Biomass_core                      init 1.442785e+03 secs
 8:                      save                    spades 1.795001e+00 secs
 9:    Biomass_borealDataPrep                      plot 8.577969e-01 secs
10:              Biomass_core                summaryBGM 3.525127e+00 secs
11:              Biomass_core      plotSummaryBySpecies 2.430483e+00 secs
12:              Biomass_core                  plotAvgs 1.400293e+00 secs
13:                      save                     later 2.052871e+00 secs
14:              Biomass_core           summaryBGMstart 1.140946e+00 secs
15:              Biomass_core                 Dispersal 2.204230e-01 secs
16:              Biomass_core cohortAgeReclassification 1.316502e-01 secs
17:              Biomass_core              summaryRegen 4.298489e-01 secs
Warning message:
In as.data.table.list(jval, .named = NULL) :
  Item 3 has 147 rows but longest item has 148; recycled with remainder.

I tracked the warning down to the line that calculates the elapsed time for each event using diff, so that the last event is getting the elapsed time of the first