Closed gregorgorjanc closed 8 months ago
❯ checking examples ... ERROR Running examples in ‘SIMplyBee-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: createCrossPlan > ### Title: Create a plan for crossing virgin queens > ### Aliases: createCrossPlan > > ### ** Examples > > founderGenomes <- quickHaplo(nInd = 1000, nChr = 1, segSites = 100) > SP <- SimParamBee$new(founderGenomes) > ## Don't show: > SP$nThreads = 1L > ## End(Don't show) > basePop <- createVirginQueens(founderGenomes) > > # Create three virgin MultiColony objects with locations > virginColonies1 <- createMultiColony(basePop[1:30]) > virginColonies1 <- setLocation(virginColonies1, + location = Map(c, runif(30, 0, 2*pi), + runif(30, 0, 2*pi))) > virginColonies2 <- createMultiColony(basePop[31:60]) > virginColonies2 <- setLocation(virginColonies2, + location = Map(c, runif(30, 0, 2*pi), + runif(30, 0, 2*pi))) > virginColonies3 <- createMultiColony(basePop[61:90]) > virginColonies3 <- setLocation(virginColonies3, + location = Map(c, runif(30, 0, 2*pi), + runif(30, 0, 2*pi))) > > # Create drone colonies > droneColonies <- createMultiColony(basePop[121:200]) > droneColonies <- setLocation(droneColonies, + location = Map(c, runif(80, 0, 2*pi), + runif(80, 0, 2*pi))) > > # Create some drones to mate initial drone colonies with > DCA <- createDrones(basePop[201:300], nInd = 20) > # Cross initial virgin drone colonies to the DCA with a random cross plan > randomCrossPlan <- createCrossPlan(x = droneColonies, + drones = DCA, + nDrones = nFathersPoisson, + spatial = FALSE) > droneColonies <- cross(droneColonies, + drones = DCA, + nDrones = nFathersPoisson, + crossPlan = randomCrossPlan) > > # Plot the colonies in space > virginLocations <- as.data.frame(getLocation(c(virginColonies1, virginColonies2, virginColonies3), + collapse= TRUE)) > virginLocations$Type <- "Virgin" > droneLocations <- as.data.frame(getLocation(droneColonies, collapse= TRUE)) > droneLocations$Type <- "Drone" > locations <- rbind(virginLocations, droneLocations) > > plot(x = locations$V1, y = locations$V2, + col = c("red", "blue")[as.numeric(as.factor(locations$Type))]) > > # Cross according to a spatial cross plan according to the colonies' locations > crossPlanSpatial <- createCrossPlan(x = virginColonies1, + droneColonies = droneColonies, + nDrones = nFathersPoisson, + spatial = TRUE, + radius = 1.5) > > # Plot the crossing for the first colony in the crossPlan > virginLocations1 <- as.data.frame(getLocation(virginColonies1, collapse= TRUE)) > virginLocations1$Type <- "Virgin" > droneLocations <- as.data.frame(getLocation(droneColonies, collapse= TRUE)) > droneLocations$Type <- "Drone" > locations1 <- rbind(virginLocations1, droneLocations) > > # Blue marks the target virgin colony and blue marks the drone colonies in the chosen radius > plot(x = locations1$V1, y = locations1$V2, pch = c(1, 2)[as.numeric(as.factor(locations1$Type))], + col = ifelse(rownames(locations1) %in% crossPlanSpatial[[1]], + "red", + ifelse(rownames(locations1) == names(crossPlanSpatial)[[1]], + "blue", "black"))) > > colonies1 <- cross(x = virginColonies1, + crossPlan = crossPlanSpatial, + droneColonies = droneColonies, + nDrones = nFathersPoisson) > nFathers(colonies1) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 17 20 16 12 13 13 16 15 15 14 18 10 10 15 12 12 16 16 11 12 9 15 17 12 15 13 27 28 29 30 14 16 14 11 > > # Cross according to a cross plan that is created internally within the cross function > # The cross plan is created at random, regardless the location of the colonies > colonies2 <- cross(x = virginColonies2, + droneColonies = droneColonies, + nDrones = nFathersPoisson, + crossPlan = "create") [1] "Cross plan, drone colonies" > > # Mate spatially with cross plan created internally by the cross function > colonies3 <- cross(x = virginColonies3, + droneColonies = droneColonies, + crossPlan = "create", + checkCross = "warning", + spatial = TRUE, + radius = 1) There are no potential crosses for some colonies! The cross() will fail unless argument checkCross is set to 'warning'. Crossing failed! Error in reQueen(x, virginQueen) : object 'virginQueen' not found Calls: cross -> cross -> reQueen -> isPop -> is Execution halted
I think @janaobsteter sorted this these days.