redoc · PredictiveEcology/SpaDES.core@59b3d5f

lintr-bot · 2018-09-14T05:13:51Z

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: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:128:22: style: Variable or function name should be lowerCamelCase.

    obj$.list$.envir$._startClockTime <- NULL
                     ^~~~~~~~~~~~~~~~

R/cache.R:235:50: style: Commas should always have a space after.

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

R/cache.R:246:50: style: Commas should always have a space after.

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

R/cache.R:296:10: style: Commented code should be removed.

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

R/cache.R:420:1: 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:448:1: style: Lines should not be more than 100 characters.

        list2env(mget(lsObjectEnv[lsObjectEnv %in% createOutputs | lsObjectEnv %in% expectsInputs], envir = object@.envir), envir = object2@.envir)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:458:12: style: Commented code should be removed.

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

R/cache.R:462:1: 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:475:10: style: Place a space before left parenthesis, except in a function call.

      for(atts in attrsToGrab) {
         ^

R/cache.R:479:9: style: Commented code should be removed.

      # attr(object2, "tags") <- attr(object, "tags")
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:480:9: style: Commented code should be removed.

      # attr(object2, "call") <- attr(object, "call")
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:481:9: style: Commented code should be removed.

      # attr(object2, "function") <- attr(object, "function")
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/cache.R:514:66: style: Variable or function name should be lowerCamelCase.

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

R/cache.R:537:48: style: Variable or function name should be lowerCamelCase.

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

R/cache.R:629:1: style: Variable or function name should be lowerCamelCase.

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

R/cache.R:656:1: style: Variable or function name should be lowerCamelCase.

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

R/cache.R:664:1: style: Variable or function name should be lowerCamelCase.

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

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

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:320:1: style: Lines should not be more than 100 characters.

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

R/code-checking.R:369:51: style: Commas should always have a space after.

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

R/code-checking.R:369:56: style: Commas should always have a space after.

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

R/code-checking.R:385:20: style: Commas should always have a space after.

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

R/code-checking.R:385:25: style: Commas should always have a space after.

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

R/code-checking.R:396:90: style: Commas should always have a space after.

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

R/code-checking.R:441:75: style: Commas should always have a space after.

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

R/code-checking.R:455:1: style: Lines should not be more than 100 characters.

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

R/code-checking.R:464:24: style: Commas should always have a space after.

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

R/code-checking.R:464:36: style: Commas should always have a space after.

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

R/code-checking.R:465:33: style: Commas should always have a space after.

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

R/code-checking.R:465:45: style: Commas should always have a space after.

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

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

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

R/code-checking.R:481:24: style: Commas should always have a space after.

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

R/code-checking.R:481:36: style: Commas should always have a space after.

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

R/code-checking.R:482:33: style: Commas should always have a space after.

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

R/code-checking.R:482:45: style: Commas should always have a space after.

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

R/code-checking.R:504:24: style: Commas should always have a space after.

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

R/code-checking.R:504:36: style: Commas should always have a space after.

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

R/code-checking.R:505:33: style: Commas should always have a space after.

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

R/code-checking.R:505:45: style: Commas should always have a space after.

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

R/code-checking.R:517:13: style: Commas should always have a space after.

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

R/code-checking.R:517:18: style: Commas should always have a space after.

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

R/code-checking.R:519:18: style: Commas should always have a space after.

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

R/code-checking.R:519:23: style: Commas should always have a space after.

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

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/downloadData.R:54:96: style: Do not place spaces around code in parentheses or square brackets.

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

R/downloadData.R:242:7: style: Commented code should be removed.

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

R/downloadData.R:243:7: style: Commented code should be removed.

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

R/downloadData.R:250:8: style: Commented code should be removed.

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

R/downloadData.R:275:27: style: Commas should always have a space after.

    chksums2 <- chksums[0,]
                          ^

R/downloadData.R:276:6: style: Commented code should be removed.

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

R/downloadData.R:279:13: style: Do not place spaces around code in parentheses or square brackets.

        if ( all( nzchar(children) & !is.na(children) ) ) {
            ^

R/downloadData.R:279:18: style: Do not place spaces around code in parentheses or square brackets.

        if ( all( nzchar(children) & !is.na(children) ) ) {
                 ^

R/downloadData.R:279:54: style: Do not place spaces around code in parentheses or square brackets.

        if ( all( nzchar(children) & !is.na(children) ) ) {
                                                     ^

R/downloadData.R:279:56: style: Do not place spaces around code in parentheses or square brackets.

        if ( all( nzchar(children) & !is.na(children) ) ) {
                                                       ^

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

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

R/helpers.R:262:1: style: Variable or function name should be lowerCamelCase.

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

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:465:55: style: Do not place spaces around code in parentheses or square brackets.

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

R/module-define.R:744:63: 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)) ) {
        ^

R/module-dependencies-class.R:171:81: style: Do not place spaces around code in parentheses or square brackets.

    if ( !all(colnames(._outputObjectsDF()) %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:163:5: style: Variable or function name should be lowerCamelCase.

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

R/module-dependencies-methods.R:195:39: 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:209:26: 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:245:79: 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:293:8: style: Commented code should be removed.

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

R/module-repository.R:305:1: 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:401:1: style: Trailing blank lines are superfluous.

R/module-repository.R:402:1: style: Trailing blank lines are superfluous.

R/moduleMetadata.R:75:6: style: Commented code should be removed.

    #metadata <- eval(parse(text = x)) # can't be used because can't evaluate start(sim)
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting-diagrams.R:78:5: style: Variable or function name should be lowerCamelCase.

    DT <- tail(completed(sim), n)
    ^~

R/plotting-diagrams.R:173:28: style: %>% should always have a space before it and a new line after it, unless the full pipeline fits on one line.

        sapply(ll, NROW) %>% sum() %>% `*`(., 26L)
                         ~~^

R/plotting-diagrams.R:325:7: style: Variable or function name should be lowerCamelCase.

      PlotRemovingDots <- function(modDia, plotFn, axes, ...,
      ^~~~~~~~~~~~~~~~

R/plotting-diagrams.R:326:36: style: Variable or function name should be lowerCamelCase.

                                   vertex.color,
                                   ^~~~~~~~~~~~

R/plotting-diagrams.R:327:36: style: Variable or function name should be lowerCamelCase.

                                   vertex.size,
                                   ^~~~~~~~~~~

R/plotting-diagrams.R:328:36: style: Variable or function name should be lowerCamelCase.

                                   vertex.size2,
                                   ^~~~~~~~~~~~

R/plotting-diagrams.R:329:36: style: Variable or function name should be lowerCamelCase.

                                   vertex.shape,
                                   ^~~~~~~~~~~~

R/plotting-diagrams.R:330:36: style: Variable or function name should be lowerCamelCase.

                                   vertex.label.cex,
                                   ^~~~~~~~~~~~~~~~

R/plotting-diagrams.R:331:36: style: Variable or function name should be lowerCamelCase.

                                   vertex.label.family,
                                   ^~~~~~~~~~~~~~~~~~~

R/plotting-diagrams.R:345:1: style: Lines should not be more than 100 characters.

          c(nchar(namesModDia)^0.8 * 10) # use exponential to stretch out, and multiplication to make all bigger
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plotting-diagrams.R:443:22: style: Only use double-quotes.

    if ((Sys.info()[['sysname']] == "Darwin") && (Sys.which("glpsol") == "")) {
                     ^~~~~~~~~

R/plotting.R:6:31: style: Variable or function name should be lowerCamelCase.

                              na.color, zero.color, length){
                              ^~~~~~~~

R/plotting.R:6:41: style: Variable or function name should be lowerCamelCase.

                              na.color, zero.color, length){
                                        ^~~~~~~~~~

R/plotting.R:37:25: style: Variable or function name should be lowerCamelCase.

                        na.color, zero.color, length) {
                        ^~~~~~~~

R/plotting.R:37:35: style: Variable or function name should be lowerCamelCase.

                        na.color, zero.color, length) {
                                  ^~~~~~~~~~

R/plotting.R:86:22: style: Put spaces around all infix operators.

      eval(parse(text=deparse(elems[[useElem]])), envir=tmp@.envir),
                    ~^~

R/plotting.R:86:56: style: Put spaces around all infix operators.

      eval(parse(text=deparse(elems[[useElem]])), envir=tmp@.envir),
                                                      ~^~

R/plotting.R:87:12: style: Put spaces around all infix operators.

      error=function(x) eval(parse(text=deparse(elems[[useElem]])), envir=envir))
          ~^~

R/plotting.R:87:40: style: Put spaces around all infix operators.

      error=function(x) eval(parse(text=deparse(elems[[useElem]])), envir=envir))
                                      ~^~

R/plotting.R:87:74: style: Put spaces around all infix operators.

      error=function(x) eval(parse(text=deparse(elems[[useElem]])), envir=envir))
                                                                        ~^~

R/POM.R:131:1: style: Lines should not be more than 100 characters.

#' @param objFnCompare Character string. Either, "MAD" or "RMSE" indicating that inside the objective
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/POM.R:191:12: style: Variable or function name should be lowerCamelCase.

           NaNRetries = NA, logObjFnVals = FALSE, weights, useLog = FALSE) {
           ^~~~~~~~~~

R/POM.R:201:25: style: Variable or function name should be lowerCamelCase.

                        NaNRetries, logObjFnVals, weights, useLog) {
                        ^~~~~~~~~~

R/POM.R:218:28: style: Variable or function name should be lowerCamelCase.

    if (is.na(NaNRetries)) NaNRetries <- 1
                           ^~~~~~~~~~

R/POM.R:242:11: style: Variable or function name should be lowerCamelCase.

          sim_ <- Copy(sim)
          ^~~~

R/POM.R:260:11: style: Variable or function name should be lowerCamelCase.

          POMFrameNum <- .grepSysCalls(sys.calls(), pattern = "POM")
          ^~~~~~~~~~~

R/POM.R:261:13: style: Commented code should be removed.

          # scallsFirstElement <- lapply(sys.calls(), function(x) x[1])
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/POM.R:262:13: style: Commented code should be removed.

          # POMFrameNum <- grep(scallsFirstElement, pattern = "POM")
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/POM.R:264:53: style: Put spaces around all infix operators.

          envPOMCalled <- sys.frame(min(POMFrameNum)-1)
                                                   ~^~

-Original file line number
+Diff line change
@@ Expand Up / @@ -1575,47 +1575,6 @@ setReplaceMethod( @@
     })
-    ################################################################################
-    #' @param package For compatibility with \code{\link[utils]{citation}}. This can be
-    #'                a \code{simList} or a character string for a package name.
-    #' @inheritParams P
-    #' @inheritParams utils::citation
-    #' @include simList-class.R
-    #' @export
-    #' @rdname simList-accessors-metadata
-    #'
-    setGeneric("citation", function(package, lib.loc = NULL, auto = NULL, module = character()) {
-      standardGeneric("citation")
-    })
-    #' @export
-    #' @rdname simList-accessors-metadata
-    setMethod("citation",
-              signature = ".simList",
-              definition = function(package, lib.loc, auto, module) {
-                if (missing(module)) {
-                  module <- current(package)
-                  if (NROW(module) == 0)
-                    module <- unlist(modules(package))
-                }
-                out <- if (length(module) > 1) {
-                  lapply(package@depends@dependencies[module], function(deps)
-                    deps@citation)
-                } else {
-                  package@depends@dependencies[[module]]@citation
-                }
-                return(out)
-              })
-    #' @export
-    #' @rdname simList-accessors-metadata
-    setMethod("citation",
-              signature = "character",
-              definition = function(package, lib.loc, auto, module) {
-                utils::citation(package = package, lib.loc = lib.loc, auto = auto)
-              })
     ################################################################################
     #' Specify paths for modules, inputs, and outputs
@@ Expand Down Expand Up / @@ -2821,3 +2780,44 @@ setMethod("documentation", @@
               })
+    ################################################################################
+    #' @param package For compatibility with \code{\link[utils]{citation}}. This can be
+    #'                a \code{simList} or a character string for a package name.
+    #' @inheritParams P
+    #' @inheritParams utils::citation
+    #' @include simList-class.R
+    #' @export
+    #' @rdname simList-accessors-metadata
+    #'
+    setGeneric("citation", function(package, lib.loc = NULL, auto = NULL, module = character()) {
+      standardGeneric("citation")
+    })
+    #' @export
+    #' @rdname simList-accessors-metadata
+    setMethod("citation",
+              signature = ".simList",
+              definition = function(package, lib.loc, auto, module) {
+                if (missing(module)) {
+                  module <- current(package)
+                  if (NROW(module) == 0)
+                    module <- unlist(modules(package))
+                }
+                out <- if (length(module) > 1) {
+                  lapply(package@depends@dependencies[module], function(deps)
+                    deps@citation)
+                } else {
+                  package@depends@dependencies[[module]]@citation
+                }
+                return(out)
+              })
+    #' @export
+    #' @rdname simList-accessors-metadata
+    setMethod("citation",
+              signature = "character",
+              definition = function(package, lib.loc, auto, module) {
+                utils::citation(package = package, lib.loc = lib.loc, auto = auto)
+              })

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