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Update appveyor_cache.txt
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@achubaty
achubaty committed May 17, 2018
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# to manually clear the cache, just make a change to this file
# 2018-02-13
# 2018-05-16

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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:49:5: style: Commented code should be removed.

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

inst/examples/example_POM.R:84:4: style: Commented code should be removed.

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

inst/examples/example_POM.R:107:34: style: Variable or function name should be lowerCamelCase.

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

inst/examples/example_POM.R:114:5: style: Variable or function name should be lowerCamelCase.

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

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

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

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

​    # cat(" ")
      ^~~~~~~~

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

​    # cat(pars)
      ^~~~~~~~~

inst/examples/example_POM.R:123:7: 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:86:1: style: Lines should not be more than 100 characters.

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

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

​      sim <- scheduleEvent(sim, time(sim) + 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) + 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 <- 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:59:1: style: Variable or function name should be lowerCamelCase.

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

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:142:1: style: Variable or function name should be lowerCamelCase.

​Init <- function(sim) {
^~~~

inst/sampleModules/fireSpread/fireSpread.R:146:3: style: Variable or function name should be lowerCamelCase.

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

inst/sampleModules/fireSpread/fireSpread.R:150:3: style: Variable or function name should be lowerCamelCase.

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

inst/sampleModules/fireSpread/fireSpread.R:153:14: style: Variable or function name should be lowerCamelCase.

​  landscapes$Fires <- Fires
             ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:159:1: style: Variable or function name should be lowerCamelCase.

​Burn <- function(sim) {
^~~~

inst/sampleModules/fireSpread/fireSpread.R:162:3: style: Variable or function name should be lowerCamelCase.

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

inst/sampleModules/fireSpread/fireSpread.R:174:14: style: Variable or function name should be lowerCamelCase.

​  landscapes$Fires <- Fires
             ^~~~~

inst/sampleModules/fireSpread/fireSpread.R:181:1: 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:55:1: style: Variable or function name should be lowerCamelCase.

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

inst/sampleModules/randomLandscapes/randomLandscapes.R:75:1: style: Lines should not be more than 100 characters.

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

inst/sampleModules/randomLandscapes/randomLandscapes.R:86:1: style: Variable or function name should be lowerCamelCase.

​Init <- function(sim) {
^~~~

inst/sampleModules/randomLandscapes/randomLandscapes.R:100:5: 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:230:50: style: Commas should always have a space after.

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

R/cache.R:241:50: style: Commas should always have a space after.

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

R/cache.R:288:10: style: Commented code should be removed.

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

R/cache.R:324:1: style: Trailing whitespace is superfluous.

​      
^~~~~~

R/cache.R:330:1: style: Trailing whitespace is superfluous.

​  
^~

R/cache.R:342:1: style: Trailing whitespace is superfluous.

​  
^~

R/cache.R:364:14: style: Commented code should be removed.

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

R/cache.R:367:1: style: Trailing whitespace is superfluous.

​  
^~

R/cache.R:377:1: style: Trailing whitespace is superfluous.

​  
^~

R/cache.R:381:1: style: Trailing whitespace is superfluous.

​  
^~

R/cache.R:419:66: style: Variable or function name should be lowerCamelCase.

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

R/cache.R:442:48: style: Variable or function name should be lowerCamelCase.

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

R/cache.R:534:1: style: Variable or function name should be lowerCamelCase.

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

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:66:1: style: Lines should not be more than 100 characters.

​      if (identical(type, "returnSim")) { # returnSim case doesn't need to parse whole function, only last Number
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:66:41: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​      if (identical(type, "returnSim")) { # returnSim case doesn't need to parse whole function, only last Number
                                        ^

R/code-checking.R:74:37: style: Put spaces around all infix operators.

​        if (is.null(parsedXAsString)>0) {
                                   ~^~

R/code-checking.R:83:1: style: Lines should not be more than 100 characters.

​            parsedXAsString <- tryCatch(parse(text = bb[seq(funStarts[yy], funEnds[yy + 1])]), error = function(yy) NULL)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:87:1: 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:91:16: style: Commented code should be removed.

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

R/code-checking.R:92:53: style: Commas should always have a space after.

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

R/code-checking.R:146:39: 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:163:1: style: Lines should not be more than 100 characters.

​      if (identical(x[[1]], quote(`<-`)) && (any(grepl(x, pattern = paste(mustAssignToSim, collapse="|"))))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:163:100: style: Put spaces around all infix operators.

​      if (identical(x[[1]], quote(`<-`)) && (any(grepl(x, pattern = paste(mustAssignToSim, collapse="|"))))) {
                                                                                                  ~^~

R/code-checking.R:170:1: style: Lines should not be more than 100 characters.

​      } else if (is.name(x[[1]]) & (any(grepl(x[[1]], pattern = paste(mustAssignToSim, collapse="|"))))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:170:96: style: Put spaces around all infix operators.

​      } else if (is.name(x[[1]]) & (any(grepl(x[[1]], pattern = paste(mustAssignToSim, collapse="|"))))) {
                                                                                              ~^~

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 = ".envir"))) {# i.e., sim@.envir
                                                             ^

R/code-checking.R:191:1: style: Lines should not be more than 100 characters.

​            if (identical(as.character(x[[2]])[1], "[") | identical(as.character(x[[2]])[1], "[[")) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:201:19: style: Place a space before left parenthesis, except in a function call.

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

R/code-checking.R:211:62: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​      if (identical(x[[1]], quote(`<-`)) && is.call(x[[2]])) { # left side function assign
                                                             ^

R/code-checking.R:216:29: style: Place a space before left parenthesis, except in a function call.

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

R/code-checking.R:234:12: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    } else { # all other cases, just return empty
           ^

R/code-checking.R:284:1: style: Lines should not be more than 100 characters.

​  allChecks <- list(simAssigns = simAssigns, simGets = simGets, returnsSim = returnsSim, assignToSim = assignToSim, fg = fg)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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:326:62: style: Put spaces around all infix operators.

​  simAssignsInDotInputObjects <- simAssigns[names(simAssigns)==".inputObjects"]
                                                            ~^~~

R/code-checking.R:327:65: style: Put spaces around all infix operators.

​  simAssignsNotInDotInputObjects <- simAssigns[names(simAssigns)!=".inputObjects"]
                                                               ~^~~

R/code-checking.R:328:53: style: Put spaces around all infix operators.

​  simGetsInDotInputObjects <- simGets[names(simGets)==".inputObjects"]
                                                   ~^~~

R/code-checking.R:329:56: style: Put spaces around all infix operators.

​  simGetsNotInDotInputObjects <- simGets[names(simGets)!=".inputObjects"]
                                                      ~^~~

R/code-checking.R:351:1: style: Lines should not be more than 100 characters.

​                                            " must assign to the sim, e.g., sim <- scheduleEvent(sim, ...)"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:360:31: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​  if (length(outputObjNames)) { #
                              ^

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

​                                              " ",verb," declared in outputObjects, ",
                                                  ^

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

​                                              " ",verb," declared in outputObjects, ",
                                                       ^

R/code-checking.R:382:51: style: Commas should always have a space after.

​                                              " ",verb," declared in inputObjects, ",
                                                  ^

R/code-checking.R:382:56: style: Commas should always have a space after.

​                                              " ",verb," declared in inputObjects, ",
                                                       ^

R/code-checking.R:383:1: style: Lines should not be more than 100 characters.

​                                              "but no default(s) ", verb, " provided in .inputObjects"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:393:90: style: Commas should always have a space after.

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

R/code-checking.R:435:1: style: Lines should not be more than 100 characters.

​                                             "\n  with base functions: ", crayon::bold(paste(hasConflicts, collapse = ", ")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:436:1: style: Lines should not be more than 100 characters.

​                                             "\n  It is a good idea to be explicit about the package sources",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:437:1: style: Lines should not be more than 100 characters.

​                                             ", e.g., ", paste(whichFnsWithPackage, collapse = ", "),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:438:1: style: Lines should not be more than 100 characters.

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

R/code-checking.R:438:107: style: Commas should always have a space after.

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

R/code-checking.R:439:1: style: Lines should not be more than 100 characters.

​                                             (e.g., don't change when on the left hand side of an assignement operator)"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:451:1: style: Lines should not be more than 100 characters.

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

R/code-checking.R:457:1: style: Lines should not be more than 100 characters.

​          .parseMessage(m, "outputObjects", paste0(paste(missingInMetadataByFn[[fn]], collapse = ", "),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:458:55: style: Commas should always have a space after.

​                                                  " ",verbs[[fn]]," assigned to sim inside ",
                                                      ^

R/code-checking.R:458:67: style: Commas should always have a space after.

​                                                  " ",verbs[[fn]]," assigned to sim inside ",
                                                                  ^

R/code-checking.R:459:1: style: Lines should not be more than 100 characters.

​                                                  fn, ", but ",verbs[[fn]]," not declared in outputObjects"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:459:64: style: Commas should always have a space after.

​                                                  fn, ", but ",verbs[[fn]]," not declared in outputObjects"
                                                               ^

R/code-checking.R:459:76: style: Commas should always have a space after.

​                                                  fn, ", but ",verbs[[fn]]," not declared in outputObjects"
                                                                           ^

R/code-checking.R:464:1: style: Lines should not be more than 100 characters.

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

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

​          .parseMessage(m, "inputObjects", paste0(paste(missingInMetadataByFn[[fn]], collapse = ", "),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:471:55: style: Commas should always have a space after.

​                                                  " ",verbs[[fn]]," assigned to sim inside ",
                                                      ^

R/code-checking.R:471:67: style: Commas should always have a space after.

​                                                  " ",verbs[[fn]]," assigned to sim inside ",
                                                                  ^

R/code-checking.R:472:1: style: Lines should not be more than 100 characters.

​                                                  fn, ", but ",verbs[[fn]]," not declared in inputObjects"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:472:64: style: Commas should always have a space after.

​                                                  fn, ", but ",verbs[[fn]]," not declared in inputObjects"
                                                               ^

R/code-checking.R:472:76: style: Commas should always have a space after.

​                                                  fn, ", but ",verbs[[fn]]," not declared in inputObjects"
                                                                           ^

R/code-checking.R:490:1: style: Lines should not be more than 100 characters.

​          .parseMessage(m, "inputObjects", paste0(paste(missingInMetadataByFn[[fn]], collapse = ", "),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:491:56: style: Commas should always have a space after.

​                                                   " ",verbs[[fn]]," used from sim inside ",
                                                       ^

R/code-checking.R:491:68: style: Commas should always have a space after.

​                                                   " ",verbs[[fn]]," used from sim inside ",
                                                                   ^

R/code-checking.R:492:1: style: Lines should not be more than 100 characters.

​                                                   fn, ", but ",verbs[[fn]]," not declared in inputObjects"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:492:65: style: Commas should always have a space after.

​                                                   fn, ", but ",verbs[[fn]]," not declared in inputObjects"
                                                                ^

R/code-checking.R:492:77: style: Commas should always have a space after.

​                                                   fn, ", but ",verbs[[fn]]," not declared in inputObjects"
                                                                            ^

R/code-checking.R:502:13: style: Commas should always have a space after.

​        " ",verb," used from sim inside ",
            ^

R/code-checking.R:502:18: style: Commas should always have a space after.

​        " ",verb," used from sim inside ",
                 ^

R/code-checking.R:504:18: style: Commas should always have a space after.

​        ", but ",verb," not declared in inputObjects"
                 ^

R/code-checking.R:504:23: style: Commas should always have a space after.

​        ", but ",verb," not declared in inputObjects"
                      ^

R/code-checking.R:572:45: style: Put spaces around all infix operators.

​  c("is", "are")[1 + as.numeric(length(item)>1)]
                                           ~^~

R/code-checking.R:622:45: style: Put spaces around all infix operators.

​    xAsString <- xAsString[length(xAsString)-1]
                                           ~^~

R/code-checking.R:637:1: style: Lines should not be more than 100 characters.

​    wh <- which(grepl(pattern = paste0("\\b", namedTxt[patternIndex], "\\b"), pd$text) & (pd$line1 == pd$line2) & (pd$token == "expr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:639:1: style: Lines should not be more than 100 characters.

​      wh <- which(agrepl(pattern = paste0(namedTxt[patternIndex]), pd$text) & (pd$line1 == pd$line2) & (pd$token == "expr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:642:1: style: Lines should not be more than 100 characters.

​    outerWh <- which(grepl(paste0("\\b", names(namedTxt)[patternIndex], "\\b"), pd$text) & (pd$token == "expr"))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/code-checking.R:644:6: style: Commented code should be removed.

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

R/code-checking.R:648:34: style: Commas should always have a space after.

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

R/code-checking.R:648:64: style: Commas should always have a space after.

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

R/code-checking.R:648:79: 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/experiment.R:200:6: style: Commented code should be removed.

​    #sim <- Copy(sim, objects = FALSE, queues = TRUE)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

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

R/experiment.R:216:7: style: Commented code should be removed.

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

R/experiment.R:218:6: style: Commented code should be removed.

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

R/experiment.R:222:11: style: Commented code should be removed.

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

R/experiment.R:314:58: style: Commented code should be removed.

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

R/helpers.R:228:74: style: Place a space before left parenthesis, except in a function call.

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

R/load.R:198:1: 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:467:55: style: Do not place spaces around code in parentheses or square brackets.

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

R/module-define.R:722:63: 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:172:9: style: Commented code should be removed.

​    #   warning("input object data.frame should use colnames sourceURL.")
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/module-dependencies-class.R:174:9: style: Do not place spaces around code in parentheses or square brackets.

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

R/module-dependencies-class.R:174:78: style: Do not place spaces around code in parentheses or square brackets.

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

R/module-dependencies-methods.R:43:5: style: Variable or function name should be lowerCamelCase.

​    DT <- .depsEdgeListMem(deps, plot)
    ^~

R/module-dependencies-methods.R:56:3: style: Variable or function name should be lowerCamelCase.

​  sim.in <- sim.out <- data.table(objectName = character(0),
  ^~~~~~

R/module-dependencies-methods.R:56:13: style: Variable or function name should be lowerCamelCase.

​  sim.in <- sim.out <- data.table(objectName = character(0),
            ^~~~~~~

R/module-dependencies-methods.R:61:7: style: Variable or function name should be lowerCamelCase.

​      z.in <- as.data.table(x@inputObjects)[, .(objectName, objectClass)]
      ^~~~

R/module-dependencies-methods.R:62:7: style: Variable or function name should be lowerCamelCase.

​      z.out <- as.data.table(x@outputObjects)[, .(objectName, objectClass)]
      ^~~~~

R/module-dependencies-methods.R:65:9: style: Variable or function name should be lowerCamelCase.

​        sim.in <<- rbindlist(list(sim.in, z.in), use.names = TRUE)
        ^~~~~~

R/module-dependencies-methods.R:68:9: style: Variable or function name should be lowerCamelCase.

​        sim.out <<- rbindlist(list(sim.out, z.out), use.names = TRUE)
        ^~~~~~~

R/module-dependencies-methods.R:80:5: style: Variable or function name should be lowerCamelCase.

​    DT <- dx[, list(from = module, to = i.module,
    ^~

R/module-dependencies-methods.R:83:15: style: Variable or function name should be lowerCamelCase.

​    if (plot) DT <- DT[!duplicated(DT[, 1:2, with = FALSE]), ]
              ^~

R/module-dependencies-methods.R:85:5: style: Variable or function name should be lowerCamelCase.

​    DT <- data.table(from = character(0), to = character(0),
    ^~

R/module-dependencies-methods.R:164:5: style: Variable or function name should be lowerCamelCase.

​    M <- distances(simGraph, mode = "out")
    ^

R/module-dependencies-methods.R:196:39: style: %>% should always have a space before it and a new line after it, unless the full pipeline fits on one line.

​      missingObjects <- simEdgeList %>% filter(from != to) %>%
                                    ~~^

R/module-dependencies-methods.R:210:26: style: %>% should always have a space before it and a new line after it, unless the full pipeline fits on one line.

​    return(newEdgeList %>% data.table() %>% setorder("from", "to", "objName"))
                       ~~^

R/module-dependencies-methods.R:246:79: style: Do not place spaces around code in parentheses or square brackets.

​              loadOrder <- names(simGraph[[tsort, ]]) %>% .[!(. %in% "_INPUT_" )]
                                                                              ^

R/module-repository.R:28:1: style: Lines should not be more than 100 characters.

​#'          (\url{http://spades-core.predictiveecology.org/articles/ii-modules.html#module-directory-structure-modulename}),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/module-repository.R:52:1: style: Lines should not be more than 100 characters.

​    zipFiles <- grep(file.path(name, "data"), zipFiles, invert = TRUE, value = TRUE) # remove any zip in data folder
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/module-repository.R:295:8: style: Commented code should be removed.

​      #versionWarning(name, version)
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/module-repository.R:307:1: style: Lines should not be more than 100 characters.

​        GET(zip, ua, config = list(config(token = pat)), write_disk(localzip, overwrite = overwrite))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/module-repository.R:403:1: style: Trailing blank lines are superfluous.

​
^

R/module-repository.R:404:1: style: Trailing blank lines are superfluous.

​
^

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