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submit v0.2.5 to CRAN

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achubaty committed Mar 19, 2019
1 parent 84b8d10 commit 1cf450efeef66eac0efaafd4da0a9ebb015b2b43
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This package was submitted to CRAN on 2019-02-11.
Once it is accepted, delete this file and tag the release (commit 86e5f7861f).
This package was submitted to CRAN on 2019-03-18.
Once it is accepted, delete this file and tag the release (commit 84b8d10e85).

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replied Mar 19, 2019

inst/examples/example_experiment.R:91:5: style: Commented code should be removed.

# library(raster)
    ^~~~~~~~~~~~~~~

inst/examples/example_experiment.R:92:5: style: Commented code should be removed.

# beginCluster(20) # if you have multiple clusters available, use them here to save time
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_experiment.R:96:5: style: Commented code should be removed.

# endCluster() # end the clusters
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_experiment.R:152:5: style: Commented code should be removed.

# fires <- lapply(sims, function(x) x$landscape$fires) %>% stack
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_POM.R:48:5: style: Commented code should be removed.

# cl <- makeCluster(detectCores() - 1) # not implemented yet in DEoptim
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_POM.R:83:4: style: Commented code should be removed.

#stopCluster(cl) # not yet implemented, waiting for DEoptim
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_POM.R:106:34: style: Variable or function name should be lowerCamelCase.

​    params(sim1)$caribouMovement$N <- pars[2]
                                 ^

inst/examples/example_POM.R:113:5: style: Variable or function name should be lowerCamelCase.

nPattern_Out <- caribouFn(out$caribou)
    ^~~~~~~~~~~~

inst/examples/example_POM.R:119:7: style: Commented code should be removed.

# cat(minimizeFn)
      ^~~~~~~~~~~~~~~

inst/examples/example_POM.R:120:7: style: Commented code should be removed.

# cat(" ")
      ^~~~~~~~

inst/examples/example_POM.R:121:7: style: Commented code should be removed.

# cat(pars)
      ^~~~~~~~~

inst/examples/example_POM.R:122:7: style: Commented code should be removed.

# cat("\n")
      ^~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:1:1: style: Variable or function name should be lowerCamelCase.

SpaDES.core.version <- "0.1.0"
^~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:54:1: style: Variable or function name should be lowerCamelCase.

doEvent.caribouMovement <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:78:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$moveInterval, "caribouMovement", "move")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:82:1: style: Lines should not be more than 100 characters.

​      Plot(sim$caribou, addTo = paste("sim", SpaDES.core::P(sim)$stackName, "habitatQuality", sep = "$"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:86:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$.plotInterval, "caribouMovement", "plot", .last())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:90:1: style: Lines should not be more than 100 characters.

​      Plot(sim$caribou, addTo = paste("sim", SpaDES.core::P(sim)$stackName, "habitatQuality", sep = "$"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:95:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$.plotInterval, "caribouMovement", "plot", .last())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:102:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$.saveInterval, "caribouMovement", "save", .last() + 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:114:1: style: Variable or function name should be lowerCamelCase.

Init <- function(sim) {
^~~~

inst/sampleModules/caribouMovement/caribouMovement.R:121:3: style: Variable or function name should be lowerCamelCase.

N <- SpaDES.core::P(sim)$N
  ^

inst/sampleModules/caribouMovement/caribouMovement.R:122:3: style: Variable or function name should be lowerCamelCase.

IDs <- as.character(1:N)
  ^~~

inst/sampleModules/caribouMovement/caribouMovement.R:138:1: style: Variable or function name should be lowerCamelCase.

Move <- function(sim) {
^~~~

inst/sampleModules/fireSpread/fireSpread.R:1:1: style: Variable or function name should be lowerCamelCase.

SpaDES.core.version <- "0.1.0"
^~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:20:1: style: Lines should not be more than 100 characters.

​    person(c("Alex", "M"), "Chubaty", email = "alexander.chubaty@canada.ca", role = c("aut", "cre")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:21:1: style: Lines should not be more than 100 characters.

​    person(c("Eliot", "J", "B"), "McIntire", email = "eliot.mcintire@canada.ca", role = c("aut", "cre")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:35:1: style: Lines should not be more than 100 characters.

​    defineParameter("persistprob", "numeric", 0.00, 0, 1, "probability of fire persisting in a pixel"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:37:1: style: Lines should not be more than 100 characters.

​    defineParameter("spreadprob", "numeric", 0.225, 0.05, 0.5, "probability of fire spreading into a pixel"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:38:1: style: Lines should not be more than 100 characters.

​    defineParameter("startTime", "numeric", start(sim) + 1, 0, end(sim), "time of initial fire ignition"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:39:1: style: Lines should not be more than 100 characters.

​    defineParameter(".plotInitialTime", "numeric", start(sim), start(sim), end(sim) + 1, "time to schedule first plot event"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:41:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInitialTime", "numeric", NA_real_, NA, NA, "time to schedule first save event"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:42:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInterval", "numeric", NA_real_, NA, NA, "time interval between save events")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:45:1: style: Lines should not be more than 100 characters.

​    expectsInput(objectName = SpaDES.core::P(sim, "fireSpread")$stackName, objectClass = "RasterStack",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:51:1: style: Lines should not be more than 100 characters.

​    createsOutput(objectName = SpaDES.core::P(sim, "fireSpread")$stackName, objectClass = "RasterStack",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:59:1: style: Variable or function name should be lowerCamelCase.

doEvent.fireSpread <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:80:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, SpaDES.core::P(sim)$.plotInitialTime, "fireSpread", "plot.init", .last())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:87:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim), "fireSpread", "stats") # do stats immediately following burn
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:88:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$returnInterval, "fireSpread", "burn")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:108:1: style: Lines should not be more than 100 characters.

stackName <- SpaDES.core::P(sim)$stackName # Plot doesn't like long names -- create local variable
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:143:1: style: Variable or function name should be lowerCamelCase.

Init <- function(sim) {
^~~~

inst/sampleModules/fireSpread/fireSpread.R:147:3: style: Variable or function name should be lowerCamelCase.

Fires <- raster(extent(landscapes), ncol = ncol(landscapes),
  ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:151:3: style: Variable or function name should be lowerCamelCase.

Fires <- setValues(Fires, 0)
  ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:154:14: style: Variable or function name should be lowerCamelCase.

landscapes$Fires <- Fires
             ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:160:1: style: Variable or function name should be lowerCamelCase.

Burn <- function(sim) {
^~~~

inst/sampleModules/fireSpread/fireSpread.R:163:3: style: Variable or function name should be lowerCamelCase.

Fires <- spread(landscapes[[1]],
  ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:175:14: style: Variable or function name should be lowerCamelCase.

landscapes$Fires <- Fires
             ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:182:1: style: Variable or function name should be lowerCamelCase.

Stats <- function(sim) {
^~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:1:1: style: Variable or function name should be lowerCamelCase.

SpaDES.core.version <- "0.1.0"
^~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:33:1: style: Lines should not be more than 100 characters.

​    defineParameter("inRAM", "logical", FALSE, TRUE, FALSE, "should the raster be stored in memory?"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:34:1: style: Lines should not be more than 100 characters.

​    defineParameter("nx", "numeric", 100L, 10L, 500L, "size of map (number of pixels) in the x dimension"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:35:1: style: Lines should not be more than 100 characters.

​    defineParameter("ny", "numeric", 100L, 10L, 500L, "size of map (number of pixels) in the y dimension"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:37:1: style: Lines should not be more than 100 characters.

​    defineParameter(".plotInitialTime", "numeric", start(sim), start(sim), NA, "time to schedule first plot event"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:38:1: style: Lines should not be more than 100 characters.

​    defineParameter(".plotInterval", "numeric", NA_real_, NA, NA, "time interval between plot events"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:39:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInitialTime", "numeric", NA_real_, NA, NA, "time to schedule first save event"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:40:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInterval", "numeric", NA_real_, NA, NA, "time interval between save events"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:41:1: style: Lines should not be more than 100 characters.

​    defineParameter(".useCache", "logical", FALSE, c("init", "plot"), NA, "should the module result be cached for future use")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:49:1: style: Lines should not be more than 100 characters.

​    createsOutput(objectName = SpaDES.core::P(sim, "randomLandscapes")$stackName, objectClass = "RasterStack",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:55:1: style: Variable or function name should be lowerCamelCase.

doEvent.randomLandscapes <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:63:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, SpaDES.core::P(sim)$.plotInitialTime, "randomLandscapes", "plot", .last())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:64:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, SpaDES.core::P(sim)$.saveInitialTime, "randomLandscapes", "save", .last() + 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:76:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$.saveInterval, "randomLandscapes", "save", .last() + 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:87:1: style: Variable or function name should be lowerCamelCase.

Init <- function(sim) {
^~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:101:3: style: Variable or function name should be lowerCamelCase.

DEM <- gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
  ^~~

inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R:17:1: style: Lines should not be more than 100 characters.

​    defineParameter(".plotInitialTime", "numeric", NA_real_, NA, NA, "This describes the simulation time at which the first plot event should occur"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R:18:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInitialTime", "numeric", NA_real_, NA, NA, "This describes the simulation time at which the first save event should occur")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:83:6: style: Commented code should be removed.

#names(envirHash) <- names(allObjsInSimList)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:132:22: style: Variable or function name should be lowerCamelCase.

obj$.list[[1]]$._startClockTime <- NULL
                     ^~~~~~~~~~~~~~~~

R/cache.R:133:22: style: Variable or function name should be lowerCamelCase.

obj$.list[[1]]$._timestamp <- NULL
                     ^~~~~~~~~~~

R/cache.R:240:50: style: Commas should always have a space after.

​          cat(crayon::blue("  Using ", fromWhere," copy of", cur$moduleName, "module\n"))
                                                 ^

R/cache.R:253:50: style: Commas should always have a space after.

​          cat(crayon::blue("  Using ", fromWhere," copy of", cur$eventType, "event in",
                                                 ^

R/cache.R:302:10: style: Commented code should be removed.

#checkPath(cacheRepo, create = TRUE) #SpaDES dependency
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:343:8: style: Commented code should be removed.

#attr(object, ".Cache")$newCache <- NULL
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:371:1: style: Lines should not be more than 100 characters.

pre <- lapply(preDigest[[whSimList]]$.list[[whSimList2]][existingObjs], fastdigest::fastdigest)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:379:6: style: Commented code should be removed.

#attr(object, ".Cache")$changed <- changed
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:452:1: style: Lines should not be more than 100 characters.

#   makes soft copy of all objects, i.e., they have the identical objects, which are pointers only
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:468:1: style: Lines should not be more than 100 characters.

createOutputs <- c(createOutputs, currModules) # add the environments for each module - allow local objects
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:484:36: style: Put spaces around all infix operators.

if (length(object2@current)==0) { # means it is not in a spades call
                                  ~^~~

R/cache.R:484:41: style: Opening curly braces should never go on their own line and should always be followed by a new line.

if (length(object2@current)==0) { # means it is not in a spades call
                                        ^

R/cache.R:493:63: style: Put spaces around all infix operators.

eventsAddedByThisModule <- events(object)$moduleName==current(object2)$moduleName
                                                             ~^~~

R/cache.R:497:42: style: Opening curly braces should never go on their own line and should always be followed by a new line.

b <- lapply(b, function(x) {x[["order"]] <- 2; x})
                                         ^

R/cache.R:500:42: style: Opening curly braces should never go on their own line and should always be followed by a new line.

d <- lapply(d, function(x) {x[["order"]] <- 1; x})
                                         ^

R/cache.R:507:1: style: Lines should not be more than 100 characters.

#              args = list(append(object@events[eventsAddedByThisModule], object2@events)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:510:56: style: Opening curly braces should never go on their own line and should always be followed by a new line.

object2@events <- lapply(f1, function(f) {f$order <- NULL; f})
                                                       ^

R/cache.R:512:1: style: Lines should not be more than 100 characters.

#                           args = list(append(object@events[eventsAddedByThisModule], object2@events)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:515:12: style: Commented code should be removed.

#object2@events <- unique(rbindlist(list(object@events, object2@events)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:519:1: style: Lines should not be more than 100 characters.

# This is for objects that are not in the return environment yet because they are unrelated to the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:532:10: style: Place a space before left parenthesis, except in a function call.

for(atts in attrsToGrab) {
         ^

R/cache.R:534:10: style: Commented code should be removed.

#attr(object2, atts) <- attr(object, atts)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:569:66: style: Variable or function name should be lowerCamelCase.

setGeneric(".addTagsToOutput", function(object, outputObjects, FUN) {
                                                                 ^~~

R/cache.R:592:48: style: Variable or function name should be lowerCamelCase.

definition = function(object, outputObjects, FUN, preDigestByClass) {
                                               ^~~

R/cache.R:603:8: style: Commented code should be removed.

#attr(outputToSave, "tags") <- attr(object, "tags")
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:604:8: style: Commented code should be removed.

#attr(outputToSave, "call") <- attr(object, "call")
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:607:11: style: Commented code should be removed.

# attr(outputToSave, "function") <- attr(object, "function")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:695:1: style: Variable or function name should be lowerCamelCase.

objSize.simList <- function(x, quick = getOption("reproducible.quick", FALSE)) {
^~~~~~~~~~~~~~~

R/cache.R:721:1: style: Variable or function name should be lowerCamelCase.

makeMemoisable.simList <- function(x) {
^~~~~~~~~~~~~~~~~~~~~~

R/cache.R:729:1: style: Variable or function name should be lowerCamelCase.

unmakeMemoisable.simList_ <- function(x) {
^~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:754:6: style: Commented code should be removed.

#attr(y, att) <- attr(x, att)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check.R:151:7: style: Commented code should be removed.

# modules <- sim@modules
      ^~~~~~~~~~~~~~~~~~~~~~

R/check.R:152:7: style: Commented code should be removed.

# userModules <- modules[-which(coreModules %in% modules)]
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/checkpoint.R:36:1: style: Variable or function name should be lowerCamelCase.

doEvent.checkpoint <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~

R/code-checking.R:86:1: style: Lines should not be more than 100 characters.

xAsCall <- .isLastLineSim(x = x, xAsString = bb[seq(funStarts[yy], funEnds[yy + 1])])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:90:16: style: Commented code should be removed.

#y = strsplit(bb[funStarts[yy]], split = "\\s+")[[1]][1]
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:91:53: style: Commas should always have a space after.

y <- paste0(cantCodeCheckMessage, "'",bb[funStarts[yy]], "'")
                                                    ^

R/code-checking.R:144:39: style: Opening curly braces should never go on their own line and should always be followed by a new line.

if (identical(type, "returnSim")) { # This is intended for only the last line of a function
                                      ^

R/code-checking.R:182:48: style: Do not place spaces around code in parentheses or square brackets.

​      } else if (identical(x[[1]], quote(`<-`)) ) {
                                               ^

R/code-checking.R:185:62: style: Opening curly braces should never go on their own line and should always be followed by a new line.

if (any(grepl(x[[2]][[2]], pattern = ".xData"))) {# i.e., sim@.xData
                                                             ^

R/code-checking.R:202:19: style: Place a space before left parenthesis, except in a function call.

x <- x[-(1:2)]
                  ^

R/code-checking.R:218:29: style: Place a space before left parenthesis, except in a function call.

x[[2]] <- x[[2]][-(1:2)]
                            ^

R/code-checking.R:319:1: style: Lines should not be more than 100 characters.

allChecks[anyCantCodeCheck] <- lapply(names(cantCodeCheck[anyCantCodeCheck]), function(objName) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:367:51: style: Commas should always have a space after.

" ",verb," declared in metadata outputObjects, ",
                                                  ^

R/code-checking.R:367:56: style: Commas should always have a space after.

" ",verb," declared in metadata outputObjects, ",
                                                       ^

R/code-checking.R:383:20: style: Commas should always have a space after.

" ",verb," declared in metadata inputObjects, ",
                   ^

R/code-checking.R:383:25: style: Commas should always have a space after.

" ",verb," declared in metadata inputObjects, ",
                        ^

R/code-checking.R:394:90: style: Commas should always have a space after.

​                                       paste0(paste(missingFrmMod, collapse = ", "), " ",verb,
                                                                                         ^

R/code-checking.R:439:75: style: Commas should always have a space after.

" but only for the 'get' functions, not the 'set' function ","
                                                                          ^

R/code-checking.R:453:1: style: Lines should not be more than 100 characters.

missingInMetadata <- simAssignsNotInDotInputObjects[!(simAssignsNotInDotInputObjects %in% outputObjNames)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:470:1: style: Lines should not be more than 100 characters.

missingInMetadata <- simAssignsInDotInputObjects[!(simAssignsInDotInputObjects %in% inputObjNames)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:662:6: style: Commented code should be removed.

#unique(pd[outerWh, "line1"])
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:666:34: style: Commas should always have a space after.

whInner <- any((pd[outerWh,"line1"] < lwf) & (pd[outerWh,"line2"] > lwf) )
                                 ^

R/code-checking.R:666:64: style: Commas should always have a space after.

whInner <- any((pd[outerWh,"line1"] < lwf) & (pd[outerWh,"line2"] > lwf) )
                                                               ^

R/code-checking.R:666:79: style: Do not place spaces around code in parentheses or square brackets.

whInner <- any((pd[outerWh,"line1"] < lwf) & (pd[outerWh,"line2"] > lwf) )
                                                                              ^

R/copy.R:37:13: style: Variable or function name should be lowerCamelCase.

sim_ <- object
            ^~~~

R/copy.R:42:14: style: Commented code should be removed.

#sim_@.xData <- new.env(parent = asNamespace("SpaDES.core"))
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/copy.R:43:14: style: Commented code should be removed.

#sim_@.xData <- new.env(parent = as.environment("package:SpaDES.core"))
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/copy.R💯1: style: Trailing blank lines are superfluous.

^

R/copy.R:101:1: style: Trailing blank lines are superfluous.

^

R/downloadData.R:55:96: style: Do not place spaces around code in parentheses or square brackets.

io <- .parseModulePartial(sim, modules = list(module), defineModuleElement = "inputObjects" )
                                                                                               ^

R/downloadData.R:245:7: style: Commented code should be removed.

# parsedModule <- parse(file = file.path(path, module, paste0(module, '.R')))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/downloadData.R:246:7: style: Commented code should be removed.

# urls <- .getSourceURL(pattern = fileToDownload, x = parsedModule)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/downloadData.R:253:8: style: Commented code should be removed.

#urls <- moduleMetadata(module, path)$inputObjects$sourceURL
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/downloadData.R:278:27: style: Commas should always have a space after.

chksums2 <- chksums[0,]
                          ^

R/downloadData.R:279:6: style: Commented code should be removed.

#children <- moduleMetadata(module, path)$childModules
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:214:7: style: Commented code should be removed.

# cl <- tryCatch(getCluster(), error = function(x) NULL)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:215:7: style: Commented code should be removed.

# on.exit(if (!is.null(cl)) returnCluster(), add = TRUE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:217:6: style: Commented code should be removed.

#if (length(modules) == 0) modules <- list(modules(sim)[-(1:4)])
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:221:11: style: Commented code should be removed.

# unlist(params[paramsTmp], recursive = FALSE)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:267:6: style: Commented code should be removed.

#cachePaths <- paste0(sim@paths$cachePath, "_", numToDo)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:278:87: style: Commas should always have a space after.

​        message("Completed a parallel cluster, returning data.table to setDTthreads(",b,")")
                                                                                      ^

R/experiment.R:278:89: style: Commas should always have a space after.

​        message("Completed a parallel cluster, returning data.table to setDTthreads(",b,")")
                                                                                        ^

R/experiment.R:282:1: style: Lines should not be more than 100 characters.

​    on.exit({try(stopCluster(cl), silent = TRUE); message("shutting down parallel nodes")}, add = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:282:13: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    on.exit({try(stopCluster(cl), silent = TRUE); message("shutting down parallel nodes")}, add = TRUE)
            ^

R/experiment.R:284:6: style: Commented code should be removed.

#dots <- list(...)
     ^~~~~~~~~~~~~~~~~

R/experiment.R:285:6: style: Commented code should be removed.

#args <- append(args, dots)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:286:6: style: Commented code should be removed.

#args <- append(args, list(sim = sim))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:287:8: style: Commented code should be removed.

#if (missing(notOlderThan)) notOlderThan <- NULL
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:288:8: style: Commented code should be removed.

#li <- list(notOlderThan = notOlderThan)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:289:8: style: Commented code should be removed.

#args <- append(args, li)
       ^~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:297:6: style: Commented code should be removed.

#expOut <- do.call(get(parFun), args)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:299:6: style: Commented code should be removed.

#lapply(cachePaths, function(from) mergeCache(cachePath(sim), from))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:300:6: style: Commented code should be removed.

#unlink(cachePaths, recursive = TRUE)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:330:1: style: Variable or function name should be lowerCamelCase.

FunDef <- function(ind, sim, factorialExp, modules, params,
^~~~~~

R/experiment.R:383:54: style: Commented code should be removed.

​        params(sim_)[[mod[x]]][[param[[x]]]] <- val #factorialExp[ind,x]
                                                     ^~~~~~~~~~~~~~~~~~~

R/experiment.R:426:7: style: Variable or function name should be lowerCamelCase.

sim_ <- sim
      ^~~~

R/experiment.R:489:4: style: Commented code should be removed.

#sim_@paths$cachePath <- cachePaths[ind]#, sim_@paths$cachePath)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:496:32: style: Remove spaces before the left parenthesis in a function call.

.optimalClusterNum <- function (memRequiredMB = 500, maxNumClusters = 1) {
                               ^

R/experiment.R:505:58: style: Put spaces around all infix operators.

numClusters <- floor(min(detectedNumCores, availMem/memRequiredMB))
                                                        ~^~

R/experiment.R:518:6: style: Commented code should be removed.

#  message("This function returns 1 cluster on Windows.")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:519:6: style: Commented code should be removed.

#  numClusters <- 1
     ^~~~~~~~~~~~~~~~

R/experiment.R:525:32: style: Remove spaces before the left parenthesis in a function call.

.makeClusterRandom <- function (..., iseed = NULL) {
                               ^

R/experiment.R:531:1: style: Lines should not be more than 100 characters.

for (i in 1:4) cat(file = dots$outfile, "------------------------------------------------------------")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:232:74: style: Place a space before left parenthesis, except in a function call.

​                             paste0("package:", .pkgEnv$corePackagesVec[-(1:2)]))
                                                                         ^

R/helpers.R:264:1: style: Variable or function name should be lowerCamelCase.

all.equal.simList <- function(target, current, ...) {
^~~~~~~~~~~~~~~~~

R/helpers.R:280:5: style: Commented code should be removed.

# suppressWarnings(rm("._startClockTime", envir = envir(target)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:281:5: style: Commented code should be removed.

# suppressWarnings(rm("._startClockTime", envir = envir(current)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:282:5: style: Commented code should be removed.

# suppressWarnings(rm("._firstEventClockTime", envir = envir(target)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:283:5: style: Commented code should be removed.

# suppressWarnings(rm("._firstEventClockTime", envir = envir(current)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:284:5: style: Commented code should be removed.

# suppressWarnings(rm(".timestamp", envir = envir(target)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:285:5: style: Commented code should be removed.

# suppressWarnings(rm(".timestamp", envir = envir(current)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/load.R:127:55: style: Commas should always have a space after.

nonNAFileList <- filelist[!is.na(filelist$file),]
                                                      ^

R/load.R:207:1: style: Lines should not be more than 100 characters.

​                names(argument) <- c(nam, names(formals(getFromNamespace(loadFun[y], loadPackage[y])))[1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/misc-methods.R:463:55: style: Do not place spaces around code in parentheses or square brackets.

​          (inherits(get(w, envir = envir), "integer")) ) {
                                                      ^

R/misc-methods.R:633:1: style: Variable or function name should be lowerCamelCase.

Paths <- .paths()
^~~~~

R/misc-methods.R:649:14: style: Variable or function name should be lowerCamelCase.

defaults$CP <- TRUE
             ^~

R/misc-methods.R:653:14: style: Variable or function name should be lowerCamelCase.

defaults$IP <- TRUE
             ^~

R/misc-methods.R:657:14: style: Variable or function name should be lowerCamelCase.

defaults$MP <- TRUE
             ^~

R/misc-methods.R:661:14: style: Variable or function name should be lowerCamelCase.

defaults$OP <- TRUE
             ^~

R/misc-methods.R:684:68: style: Commas should never have a space before.

if (!defaults$MP) paste0("    spades.modulePath = '" , modPaths, "'\n"),
                                                                  ~^

R/misc-methods.R:700:1: style: Trailing blank lines are superfluous.

^

R/module-define.R:743:63: style: Do not place spaces around code in parentheses or square brackets.

exts <- na.omit(match(file_ext(fl), .fileExts[, "exts"]) )
                                                              ^

R/module-dependencies-class.R:53:13: style: Variable or function name should be lowerCamelCase.

out.df <- data.frame(
            ^~~~~~

R/module-dependencies-class.R:171:9: style: Do not place spaces around code in parentheses or square brackets.

if ( !all(colnames(._outputObjectsDF()) %in% colnames(object@outputObjects)) ) {
        ^
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replied Mar 19, 2019

inst/examples/example_experiment.R:91:5: style: Commented code should be removed.

# library(raster)
    ^~~~~~~~~~~~~~~

inst/examples/example_experiment.R:92:5: style: Commented code should be removed.

# beginCluster(20) # if you have multiple clusters available, use them here to save time
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_experiment.R:96:5: style: Commented code should be removed.

# endCluster() # end the clusters
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_experiment.R:152:5: style: Commented code should be removed.

# fires <- lapply(sims, function(x) x$landscape$fires) %>% stack
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_POM.R:48:5: style: Commented code should be removed.

# cl <- makeCluster(detectCores() - 1) # not implemented yet in DEoptim
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_POM.R:83:4: style: Commented code should be removed.

#stopCluster(cl) # not yet implemented, waiting for DEoptim
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/examples/example_POM.R:106:34: style: Variable or function name should be lowerCamelCase.

​    params(sim1)$caribouMovement$N <- pars[2]
                                 ^

inst/examples/example_POM.R:113:5: style: Variable or function name should be lowerCamelCase.

nPattern_Out <- caribouFn(out$caribou)
    ^~~~~~~~~~~~

inst/examples/example_POM.R:119:7: style: Commented code should be removed.

# cat(minimizeFn)
      ^~~~~~~~~~~~~~~

inst/examples/example_POM.R:120:7: style: Commented code should be removed.

# cat(" ")
      ^~~~~~~~

inst/examples/example_POM.R:121:7: style: Commented code should be removed.

# cat(pars)
      ^~~~~~~~~

inst/examples/example_POM.R:122:7: style: Commented code should be removed.

# cat("\n")
      ^~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:1:1: style: Variable or function name should be lowerCamelCase.

SpaDES.core.version <- "0.1.0"
^~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:54:1: style: Variable or function name should be lowerCamelCase.

doEvent.caribouMovement <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:78:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$moveInterval, "caribouMovement", "move")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:82:1: style: Lines should not be more than 100 characters.

​      Plot(sim$caribou, addTo = paste("sim", SpaDES.core::P(sim)$stackName, "habitatQuality", sep = "$"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:86:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$.plotInterval, "caribouMovement", "plot", .last())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:90:1: style: Lines should not be more than 100 characters.

​      Plot(sim$caribou, addTo = paste("sim", SpaDES.core::P(sim)$stackName, "habitatQuality", sep = "$"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:95:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$.plotInterval, "caribouMovement", "plot", .last())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:102:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$.saveInterval, "caribouMovement", "save", .last() + 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/caribouMovement/caribouMovement.R:114:1: style: Variable or function name should be lowerCamelCase.

Init <- function(sim) {
^~~~

inst/sampleModules/caribouMovement/caribouMovement.R:121:3: style: Variable or function name should be lowerCamelCase.

N <- SpaDES.core::P(sim)$N
  ^

inst/sampleModules/caribouMovement/caribouMovement.R:122:3: style: Variable or function name should be lowerCamelCase.

IDs <- as.character(1:N)
  ^~~

inst/sampleModules/caribouMovement/caribouMovement.R:138:1: style: Variable or function name should be lowerCamelCase.

Move <- function(sim) {
^~~~

inst/sampleModules/fireSpread/fireSpread.R:1:1: style: Variable or function name should be lowerCamelCase.

SpaDES.core.version <- "0.1.0"
^~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:20:1: style: Lines should not be more than 100 characters.

​    person(c("Alex", "M"), "Chubaty", email = "alexander.chubaty@canada.ca", role = c("aut", "cre")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:21:1: style: Lines should not be more than 100 characters.

​    person(c("Eliot", "J", "B"), "McIntire", email = "eliot.mcintire@canada.ca", role = c("aut", "cre")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:35:1: style: Lines should not be more than 100 characters.

​    defineParameter("persistprob", "numeric", 0.00, 0, 1, "probability of fire persisting in a pixel"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:37:1: style: Lines should not be more than 100 characters.

​    defineParameter("spreadprob", "numeric", 0.225, 0.05, 0.5, "probability of fire spreading into a pixel"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:38:1: style: Lines should not be more than 100 characters.

​    defineParameter("startTime", "numeric", start(sim) + 1, 0, end(sim), "time of initial fire ignition"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:39:1: style: Lines should not be more than 100 characters.

​    defineParameter(".plotInitialTime", "numeric", start(sim), start(sim), end(sim) + 1, "time to schedule first plot event"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:41:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInitialTime", "numeric", NA_real_, NA, NA, "time to schedule first save event"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:42:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInterval", "numeric", NA_real_, NA, NA, "time interval between save events")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:45:1: style: Lines should not be more than 100 characters.

​    expectsInput(objectName = SpaDES.core::P(sim, "fireSpread")$stackName, objectClass = "RasterStack",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:51:1: style: Lines should not be more than 100 characters.

​    createsOutput(objectName = SpaDES.core::P(sim, "fireSpread")$stackName, objectClass = "RasterStack",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:59:1: style: Variable or function name should be lowerCamelCase.

doEvent.fireSpread <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:80:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, SpaDES.core::P(sim)$.plotInitialTime, "fireSpread", "plot.init", .last())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:87:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim), "fireSpread", "stats") # do stats immediately following burn
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:88:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$returnInterval, "fireSpread", "burn")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:108:1: style: Lines should not be more than 100 characters.

stackName <- SpaDES.core::P(sim)$stackName # Plot doesn't like long names -- create local variable
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/fireSpread/fireSpread.R:143:1: style: Variable or function name should be lowerCamelCase.

Init <- function(sim) {
^~~~

inst/sampleModules/fireSpread/fireSpread.R:147:3: style: Variable or function name should be lowerCamelCase.

Fires <- raster(extent(landscapes), ncol = ncol(landscapes),
  ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:151:3: style: Variable or function name should be lowerCamelCase.

Fires <- setValues(Fires, 0)
  ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:154:14: style: Variable or function name should be lowerCamelCase.

landscapes$Fires <- Fires
             ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:160:1: style: Variable or function name should be lowerCamelCase.

Burn <- function(sim) {
^~~~

inst/sampleModules/fireSpread/fireSpread.R:163:3: style: Variable or function name should be lowerCamelCase.

Fires <- spread(landscapes[[1]],
  ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:175:14: style: Variable or function name should be lowerCamelCase.

landscapes$Fires <- Fires
             ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:182:1: style: Variable or function name should be lowerCamelCase.

Stats <- function(sim) {
^~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:1:1: style: Variable or function name should be lowerCamelCase.

SpaDES.core.version <- "0.1.0"
^~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:33:1: style: Lines should not be more than 100 characters.

​    defineParameter("inRAM", "logical", FALSE, TRUE, FALSE, "should the raster be stored in memory?"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:34:1: style: Lines should not be more than 100 characters.

​    defineParameter("nx", "numeric", 100L, 10L, 500L, "size of map (number of pixels) in the x dimension"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:35:1: style: Lines should not be more than 100 characters.

​    defineParameter("ny", "numeric", 100L, 10L, 500L, "size of map (number of pixels) in the y dimension"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:37:1: style: Lines should not be more than 100 characters.

​    defineParameter(".plotInitialTime", "numeric", start(sim), start(sim), NA, "time to schedule first plot event"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:38:1: style: Lines should not be more than 100 characters.

​    defineParameter(".plotInterval", "numeric", NA_real_, NA, NA, "time interval between plot events"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:39:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInitialTime", "numeric", NA_real_, NA, NA, "time to schedule first save event"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:40:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInterval", "numeric", NA_real_, NA, NA, "time interval between save events"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:41:1: style: Lines should not be more than 100 characters.

​    defineParameter(".useCache", "logical", FALSE, c("init", "plot"), NA, "should the module result be cached for future use")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:49:1: style: Lines should not be more than 100 characters.

​    createsOutput(objectName = SpaDES.core::P(sim, "randomLandscapes")$stackName, objectClass = "RasterStack",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:55:1: style: Variable or function name should be lowerCamelCase.

doEvent.randomLandscapes <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:63:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, SpaDES.core::P(sim)$.plotInitialTime, "randomLandscapes", "plot", .last())
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:64:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, SpaDES.core::P(sim)$.saveInitialTime, "randomLandscapes", "save", .last() + 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:76:1: style: Lines should not be more than 100 characters.

sim <- scheduleEvent(sim, time(sim) + SpaDES.core::P(sim)$.saveInterval, "randomLandscapes", "save", .last() + 1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:87:1: style: Variable or function name should be lowerCamelCase.

Init <- function(sim) {
^~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:101:3: style: Variable or function name should be lowerCamelCase.

DEM <- gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
  ^~~

inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R:17:1: style: Lines should not be more than 100 characters.

​    defineParameter(".plotInitialTime", "numeric", NA_real_, NA, NA, "This describes the simulation time at which the first plot event should occur"),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/sampleModules/SpaDES_sampleModules/SpaDES_sampleModules.R:18:1: style: Lines should not be more than 100 characters.

​    defineParameter(".saveInitialTime", "numeric", NA_real_, NA, NA, "This describes the simulation time at which the first save event should occur")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:83:6: style: Commented code should be removed.

#names(envirHash) <- names(allObjsInSimList)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:132:22: style: Variable or function name should be lowerCamelCase.

obj$.list[[1]]$._startClockTime <- NULL
                     ^~~~~~~~~~~~~~~~

R/cache.R:133:22: style: Variable or function name should be lowerCamelCase.

obj$.list[[1]]$._timestamp <- NULL
                     ^~~~~~~~~~~

R/cache.R:240:50: style: Commas should always have a space after.

​          cat(crayon::blue("  Using ", fromWhere," copy of", cur$moduleName, "module\n"))
                                                 ^

R/cache.R:253:50: style: Commas should always have a space after.

​          cat(crayon::blue("  Using ", fromWhere," copy of", cur$eventType, "event in",
                                                 ^

R/cache.R:302:10: style: Commented code should be removed.

#checkPath(cacheRepo, create = TRUE) #SpaDES dependency
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:343:8: style: Commented code should be removed.

#attr(object, ".Cache")$newCache <- NULL
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:371:1: style: Lines should not be more than 100 characters.

pre <- lapply(preDigest[[whSimList]]$.list[[whSimList2]][existingObjs], fastdigest::fastdigest)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:379:6: style: Commented code should be removed.

#attr(object, ".Cache")$changed <- changed
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:452:1: style: Lines should not be more than 100 characters.

#   makes soft copy of all objects, i.e., they have the identical objects, which are pointers only
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:468:1: style: Lines should not be more than 100 characters.

createOutputs <- c(createOutputs, currModules) # add the environments for each module - allow local objects
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:484:36: style: Put spaces around all infix operators.

if (length(object2@current)==0) { # means it is not in a spades call
                                  ~^~~

R/cache.R:484:41: style: Opening curly braces should never go on their own line and should always be followed by a new line.

if (length(object2@current)==0) { # means it is not in a spades call
                                        ^

R/cache.R:493:63: style: Put spaces around all infix operators.

eventsAddedByThisModule <- events(object)$moduleName==current(object2)$moduleName
                                                             ~^~~

R/cache.R:497:42: style: Opening curly braces should never go on their own line and should always be followed by a new line.

b <- lapply(b, function(x) {x[["order"]] <- 2; x})
                                         ^

R/cache.R:500:42: style: Opening curly braces should never go on their own line and should always be followed by a new line.

d <- lapply(d, function(x) {x[["order"]] <- 1; x})
                                         ^

R/cache.R:507:1: style: Lines should not be more than 100 characters.

#              args = list(append(object@events[eventsAddedByThisModule], object2@events)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:510:56: style: Opening curly braces should never go on their own line and should always be followed by a new line.

object2@events <- lapply(f1, function(f) {f$order <- NULL; f})
                                                       ^

R/cache.R:512:1: style: Lines should not be more than 100 characters.

#                           args = list(append(object@events[eventsAddedByThisModule], object2@events)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:515:12: style: Commented code should be removed.

#object2@events <- unique(rbindlist(list(object@events, object2@events)))
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:519:1: style: Lines should not be more than 100 characters.

# This is for objects that are not in the return environment yet because they are unrelated to the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:532:10: style: Place a space before left parenthesis, except in a function call.

for(atts in attrsToGrab) {
         ^

R/cache.R:534:10: style: Commented code should be removed.

#attr(object2, atts) <- attr(object, atts)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:569:66: style: Variable or function name should be lowerCamelCase.

setGeneric(".addTagsToOutput", function(object, outputObjects, FUN) {
                                                                 ^~~

R/cache.R:592:48: style: Variable or function name should be lowerCamelCase.

definition = function(object, outputObjects, FUN, preDigestByClass) {
                                               ^~~

R/cache.R:603:8: style: Commented code should be removed.

#attr(outputToSave, "tags") <- attr(object, "tags")
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:604:8: style: Commented code should be removed.

#attr(outputToSave, "call") <- attr(object, "call")
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:607:11: style: Commented code should be removed.

# attr(outputToSave, "function") <- attr(object, "function")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:695:1: style: Variable or function name should be lowerCamelCase.

objSize.simList <- function(x, quick = getOption("reproducible.quick", FALSE)) {
^~~~~~~~~~~~~~~

R/cache.R:721:1: style: Variable or function name should be lowerCamelCase.

makeMemoisable.simList <- function(x) {
^~~~~~~~~~~~~~~~~~~~~~

R/cache.R:729:1: style: Variable or function name should be lowerCamelCase.

unmakeMemoisable.simList_ <- function(x) {
^~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:754:6: style: Commented code should be removed.

#attr(y, att) <- attr(x, att)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/check.R:151:7: style: Commented code should be removed.

# modules <- sim@modules
      ^~~~~~~~~~~~~~~~~~~~~~

R/check.R:152:7: style: Commented code should be removed.

# userModules <- modules[-which(coreModules %in% modules)]
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/checkpoint.R:36:1: style: Variable or function name should be lowerCamelCase.

doEvent.checkpoint <- function(sim, eventTime, eventType, debug = FALSE) {
^~~~~~~~~~~~~~~~~~

R/code-checking.R:86:1: style: Lines should not be more than 100 characters.

xAsCall <- .isLastLineSim(x = x, xAsString = bb[seq(funStarts[yy], funEnds[yy + 1])])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:90:16: style: Commented code should be removed.

#y = strsplit(bb[funStarts[yy]], split = "\\s+")[[1]][1]
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:91:53: style: Commas should always have a space after.

y <- paste0(cantCodeCheckMessage, "'",bb[funStarts[yy]], "'")
                                                    ^

R/code-checking.R:144:39: style: Opening curly braces should never go on their own line and should always be followed by a new line.

if (identical(type, "returnSim")) { # This is intended for only the last line of a function
                                      ^

R/code-checking.R:182:48: style: Do not place spaces around code in parentheses or square brackets.

​      } else if (identical(x[[1]], quote(`<-`)) ) {
                                               ^

R/code-checking.R:185:62: style: Opening curly braces should never go on their own line and should always be followed by a new line.

if (any(grepl(x[[2]][[2]], pattern = ".xData"))) {# i.e., sim@.xData
                                                             ^

R/code-checking.R:202:19: style: Place a space before left parenthesis, except in a function call.

x <- x[-(1:2)]
                  ^

R/code-checking.R:218:29: style: Place a space before left parenthesis, except in a function call.

x[[2]] <- x[[2]][-(1:2)]
                            ^

R/code-checking.R:319:1: style: Lines should not be more than 100 characters.

allChecks[anyCantCodeCheck] <- lapply(names(cantCodeCheck[anyCantCodeCheck]), function(objName) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:367:51: style: Commas should always have a space after.

" ",verb," declared in metadata outputObjects, ",
                                                  ^

R/code-checking.R:367:56: style: Commas should always have a space after.

" ",verb," declared in metadata outputObjects, ",
                                                       ^

R/code-checking.R:383:20: style: Commas should always have a space after.

" ",verb," declared in metadata inputObjects, ",
                   ^

R/code-checking.R:383:25: style: Commas should always have a space after.

" ",verb," declared in metadata inputObjects, ",
                        ^

R/code-checking.R:394:90: style: Commas should always have a space after.

​                                       paste0(paste(missingFrmMod, collapse = ", "), " ",verb,
                                                                                         ^

R/code-checking.R:439:75: style: Commas should always have a space after.

" but only for the 'get' functions, not the 'set' function ","
                                                                          ^

R/code-checking.R:453:1: style: Lines should not be more than 100 characters.

missingInMetadata <- simAssignsNotInDotInputObjects[!(simAssignsNotInDotInputObjects %in% outputObjNames)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:470:1: style: Lines should not be more than 100 characters.

missingInMetadata <- simAssignsInDotInputObjects[!(simAssignsInDotInputObjects %in% inputObjNames)]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:662:6: style: Commented code should be removed.

#unique(pd[outerWh, "line1"])
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:666:34: style: Commas should always have a space after.

whInner <- any((pd[outerWh,"line1"] < lwf) & (pd[outerWh,"line2"] > lwf) )
                                 ^

R/code-checking.R:666:64: style: Commas should always have a space after.

whInner <- any((pd[outerWh,"line1"] < lwf) & (pd[outerWh,"line2"] > lwf) )
                                                               ^

R/code-checking.R:666:79: style: Do not place spaces around code in parentheses or square brackets.

whInner <- any((pd[outerWh,"line1"] < lwf) & (pd[outerWh,"line2"] > lwf) )
                                                                              ^

R/copy.R:37:13: style: Variable or function name should be lowerCamelCase.

sim_ <- object
            ^~~~

R/copy.R:42:14: style: Commented code should be removed.

#sim_@.xData <- new.env(parent = asNamespace("SpaDES.core"))
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/copy.R:43:14: style: Commented code should be removed.

#sim_@.xData <- new.env(parent = as.environment("package:SpaDES.core"))
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/copy.R💯1: style: Trailing blank lines are superfluous.

^

R/copy.R:101:1: style: Trailing blank lines are superfluous.

^

R/downloadData.R:55:96: style: Do not place spaces around code in parentheses or square brackets.

io <- .parseModulePartial(sim, modules = list(module), defineModuleElement = "inputObjects" )
                                                                                               ^

R/downloadData.R:245:7: style: Commented code should be removed.

# parsedModule <- parse(file = file.path(path, module, paste0(module, '.R')))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/downloadData.R:246:7: style: Commented code should be removed.

# urls <- .getSourceURL(pattern = fileToDownload, x = parsedModule)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/downloadData.R:253:8: style: Commented code should be removed.

#urls <- moduleMetadata(module, path)$inputObjects$sourceURL
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/downloadData.R:278:27: style: Commas should always have a space after.

chksums2 <- chksums[0,]
                          ^

R/downloadData.R:279:6: style: Commented code should be removed.

#children <- moduleMetadata(module, path)$childModules
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:214:7: style: Commented code should be removed.

# cl <- tryCatch(getCluster(), error = function(x) NULL)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:215:7: style: Commented code should be removed.

# on.exit(if (!is.null(cl)) returnCluster(), add = TRUE)
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:217:6: style: Commented code should be removed.

#if (length(modules) == 0) modules <- list(modules(sim)[-(1:4)])
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:221:11: style: Commented code should be removed.

# unlist(params[paramsTmp], recursive = FALSE)
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:267:6: style: Commented code should be removed.

#cachePaths <- paste0(sim@paths$cachePath, "_", numToDo)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:278:87: style: Commas should always have a space after.

​        message("Completed a parallel cluster, returning data.table to setDTthreads(",b,")")
                                                                                      ^

R/experiment.R:278:89: style: Commas should always have a space after.

​        message("Completed a parallel cluster, returning data.table to setDTthreads(",b,")")
                                                                                        ^

R/experiment.R:282:1: style: Lines should not be more than 100 characters.

​    on.exit({try(stopCluster(cl), silent = TRUE); message("shutting down parallel nodes")}, add = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:282:13: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    on.exit({try(stopCluster(cl), silent = TRUE); message("shutting down parallel nodes")}, add = TRUE)
            ^

R/experiment.R:284:6: style: Commented code should be removed.

#dots <- list(...)
     ^~~~~~~~~~~~~~~~~

R/experiment.R:285:6: style: Commented code should be removed.

#args <- append(args, dots)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:286:6: style: Commented code should be removed.

#args <- append(args, list(sim = sim))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:287:8: style: Commented code should be removed.

#if (missing(notOlderThan)) notOlderThan <- NULL
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:288:8: style: Commented code should be removed.

#li <- list(notOlderThan = notOlderThan)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:289:8: style: Commented code should be removed.

#args <- append(args, li)
       ^~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:297:6: style: Commented code should be removed.

#expOut <- do.call(get(parFun), args)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:299:6: style: Commented code should be removed.

#lapply(cachePaths, function(from) mergeCache(cachePath(sim), from))
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:300:6: style: Commented code should be removed.

#unlink(cachePaths, recursive = TRUE)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:330:1: style: Variable or function name should be lowerCamelCase.

FunDef <- function(ind, sim, factorialExp, modules, params,
^~~~~~

R/experiment.R:383:54: style: Commented code should be removed.

​        params(sim_)[[mod[x]]][[param[[x]]]] <- val #factorialExp[ind,x]
                                                     ^~~~~~~~~~~~~~~~~~~

R/experiment.R:426:7: style: Variable or function name should be lowerCamelCase.

sim_ <- sim
      ^~~~

R/experiment.R:489:4: style: Commented code should be removed.

#sim_@paths$cachePath <- cachePaths[ind]#, sim_@paths$cachePath)
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:496:32: style: Remove spaces before the left parenthesis in a function call.

.optimalClusterNum <- function (memRequiredMB = 500, maxNumClusters = 1) {
                               ^

R/experiment.R:505:58: style: Put spaces around all infix operators.

numClusters <- floor(min(detectedNumCores, availMem/memRequiredMB))
                                                        ~^~

R/experiment.R:518:6: style: Commented code should be removed.

#  message("This function returns 1 cluster on Windows.")
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/experiment.R:519:6: style: Commented code should be removed.

#  numClusters <- 1
     ^~~~~~~~~~~~~~~~

R/experiment.R:525:32: style: Remove spaces before the left parenthesis in a function call.

.makeClusterRandom <- function (..., iseed = NULL) {
                               ^

R/experiment.R:531:1: style: Lines should not be more than 100 characters.

for (i in 1:4) cat(file = dots$outfile, "------------------------------------------------------------")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:232:74: style: Place a space before left parenthesis, except in a function call.

​                             paste0("package:", .pkgEnv$corePackagesVec[-(1:2)]))
                                                                         ^

R/helpers.R:264:1: style: Variable or function name should be lowerCamelCase.

all.equal.simList <- function(target, current, ...) {
^~~~~~~~~~~~~~~~~

R/helpers.R:280:5: style: Commented code should be removed.

# suppressWarnings(rm("._startClockTime", envir = envir(target)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:281:5: style: Commented code should be removed.

# suppressWarnings(rm("._startClockTime", envir = envir(current)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:282:5: style: Commented code should be removed.

# suppressWarnings(rm("._firstEventClockTime", envir = envir(target)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:283:5: style: Commented code should be removed.

# suppressWarnings(rm("._firstEventClockTime", envir = envir(current)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:284:5: style: Commented code should be removed.

# suppressWarnings(rm(".timestamp", envir = envir(target)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/helpers.R:285:5: style: Commented code should be removed.

# suppressWarnings(rm(".timestamp", envir = envir(current)))
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/load.R:127:55: style: Commas should always have a space after.

nonNAFileList <- filelist[!is.na(filelist$file),]
                                                      ^

R/load.R:207:1: style: Lines should not be more than 100 characters.

​                names(argument) <- c(nam, names(formals(getFromNamespace(loadFun[y], loadPackage[y])))[1])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/misc-methods.R:463:55: style: Do not place spaces around code in parentheses or square brackets.

​          (inherits(get(w, envir = envir), "integer")) ) {
                                                      ^

R/misc-methods.R:633:1: style: Variable or function name should be lowerCamelCase.

Paths <- .paths()
^~~~~

R/misc-methods.R:649:14: style: Variable or function name should be lowerCamelCase.

defaults$CP <- TRUE
             ^~

R/misc-methods.R:653:14: style: Variable or function name should be lowerCamelCase.

defaults$IP <- TRUE
             ^~

R/misc-methods.R:657:14: style: Variable or function name should be lowerCamelCase.

defaults$MP <- TRUE
             ^~

R/misc-methods.R:661:14: style: Variable or function name should be lowerCamelCase.

defaults$OP <- TRUE
             ^~

R/misc-methods.R:684:68: style: Commas should never have a space before.

if (!defaults$MP) paste0("    spades.modulePath = '" , modPaths, "'\n"),
                                                                  ~^

R/misc-methods.R:700:1: style: Trailing blank lines are superfluous.

^

R/module-define.R:743:63: style: Do not place spaces around code in parentheses or square brackets.

exts <- na.omit(match(file_ext(fl), .fileExts[, "exts"]) )
                                                              ^

R/module-dependencies-class.R:53:13: style: Variable or function name should be lowerCamelCase.

out.df <- data.frame(
            ^~~~~~

R/module-dependencies-class.R:171:9: style: Do not place spaces around code in parentheses or square brackets.

if ( !all(colnames(._outputObjectsDF()) %in% colnames(object@outputObjects)) ) {
        ^
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