CRAN Package Check Results for Package SpaDES.core

Last updated on 2019-02-18 07:49:58 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.4 40.86 0.02 40.88 FAIL
r-devel-linux-x86_64-debian-gcc 0.2.4 33.19 0.01 33.20 FAIL
r-devel-linux-x86_64-fedora-clang 0.2.4 2984.83 ERROR
r-devel-linux-x86_64-fedora-gcc 0.2.4 2981.00 ERROR
r-devel-windows-ix86+x86_64 0.2.4 79.00 0.00 79.00 OK
r-patched-linux-x86_64 0.2.4 37.78 1393.57 1431.35 ERROR
r-patched-solaris-x86 0.2.4 585.60 ERROR
r-release-linux-x86_64 0.2.4 ERROR
r-release-windows-ix86+x86_64 0.2.4 47.00 402.00 449.00 OK
r-release-osx-x86_64 0.2.4 WARN
r-oldrel-windows-ix86+x86_64 0.2.4 52.00 0.00 52.00 OK
r-oldrel-osx-x86_64 0.2.4 WARN

Check Details

Version: 0.2.4
Check: tests
Result: ERROR
     Running ‘test-all.R’ [10m/11m]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("SpaDES.core")
     Loading required package: SpaDES.core
     Loading required package: quickPlot
     Loading required package: reproducible
    
     Attaching package: 'SpaDES.core'
    
     The following objects are masked from 'package:stats':
    
     end, start
    
     The following object is masked from 'package:utils':
    
     citation
    
     Killed
Flavors: r-devel-linux-x86_64-debian-clang, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.2.4
Check: re-building of vignette outputs
Result: FAIL
    
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 0.2.4
Check: tests
Result: ERROR
     Running ‘test-all.R’ [10m/13m]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("SpaDES.core")
     Loading required package: SpaDES.core
     Loading required package: quickPlot
     Loading required package: reproducible
    
     Attaching package: 'SpaDES.core'
    
     The following objects are masked from 'package:stats':
    
     end, start
    
     The following object is masked from 'package:utils':
    
     citation
    
     Killed
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.4
Check: tests
Result: ERROR
     Running ‘test-all.R’ [30m/33m]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("SpaDES.core")
     Loading required package: SpaDES.core
     Loading required package: quickPlot
     Loading required package: reproducible
    
     Attaching package: 'SpaDES.core'
    
     The following objects are masked from 'package:stats':
    
     end, start
    
     The following object is masked from 'package:utils':
    
     citation
    
     OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
     OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
     Using cached copy of .inputObjects event in test module.
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘i-introduction.Rmd’ using rmarkdown
    --- finished re-building ‘i-introduction.Rmd’
    
    --- re-building ‘ii-modules.Rmd’ using rmarkdown
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: quickPlot
    Loading required package: reproducible
    
    Attaching package: 'SpaDES.core'
    
    The following objects are masked from 'package:stats':
    
     end, start
    
    The following object is masked from 'package:utils':
    
     citation
    
    Loading required package: SpaDES.tools
    Loading required package: RandomFields
    Loading required package: sp
    Loading required package: RandomFieldsUtils
    
    Attaching package: 'RandomFields'
    
    The following object is masked from 'package:RandomFieldsUtils':
    
     RFoptions
    
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpafOwDG/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp4EmcXA/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp4EmcXA/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
    OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpafOwDG/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp4EmcXA/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp4EmcXA/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpafOwDG/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp4EmcXA/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp4EmcXA/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpafOwDG/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp4EmcXA/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp4EmcXA/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    Setting:
     options(
     spades.outputPath = '/tmp/Rtmpx34Ly4/simOutputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpafOwDG/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp4EmcXA/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpx34Ly4/simOutputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    --- finished re-building ‘ii-modules.Rmd’
    
    Warning: elapsed-time limit of 30 minutes reached for sub-process
    --- re-building ‘iii-cache.Rmd’ using rmarkdown
    Loading required package: sp
    
    Attaching package: 'raster'
    
    The following object is masked from 'package:magrittr':
    
     extract
    
    Loading required package: quickPlot
    Loading required package: reproducible
    
    Attaching package: 'SpaDES.core'
    
    The following objects are masked from 'package:stats':
    
     end, start
    
    The following object is masked from 'package:utils':
    
     citation
    
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpafOwDG/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp4EmcXA/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp4EmcXA/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
    OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
    ###### Module Code Checking - Still experimental - please report problems ########
    /data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules/randomLandscapes/randomLandscapes.R
    randomLandscapes: defineParameter: '.useCache' is not of specified type 'logical'.
    randomLandscapes: inputObjects: stackName is used from sim inside doEvent.randomLandscapes, but is not declared in metadata inputObjects
    /data/gannet/ripley/R/packages/tests-clang/SpaDES.core.Rcheck/SpaDES.core/sampleModules/fireSpread/fireSpread.R
    fireSpread: module code: landscape, testStats are declared in metadata inputObjects, but no default(s) are provided in .inputObjects
    fireSpread: inputObjects: stackName, DEM, Fires are used from sim inside doEvent.fireSpread, but are not declared in metadata inputObjects
    ###### Module Code Checking ########
    SUMMARY: processing the following file failed:
     ‘iii-cache.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.4
Check: tests
Result: ERROR
     Running ‘test-all.R’ [30m/33m]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("SpaDES.core")
     Loading required package: SpaDES.core
     Loading required package: quickPlot
     Loading required package: reproducible
    
     Attaching package: 'SpaDES.core'
    
     The following objects are masked from 'package:stats':
    
     end, start
    
     The following object is masked from 'package:utils':
    
     citation
    
     Using cached copy of .inputObjects event in test module.
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘i-introduction.Rmd’ using rmarkdown
    --- finished re-building ‘i-introduction.Rmd’
    
    --- re-building ‘ii-modules.Rmd’ using rmarkdown
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: quickPlot
    Loading required package: reproducible
    
    Attaching package: 'SpaDES.core'
    
    The following objects are masked from 'package:stats':
    
     end, start
    
    The following object is masked from 'package:utils':
    
     citation
    
    Loading required package: SpaDES.tools
    Loading required package: RandomFields
    Loading required package: sp
    Loading required package: RandomFieldsUtils
    
    Attaching package: 'RandomFields'
    
    The following object is masked from 'package:RandomFieldsUtils':
    
     RFoptions
    
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmprtPal0/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp8YPt8s/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp8YPt8s/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmprtPal0/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp8YPt8s/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp8YPt8s/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmprtPal0/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp8YPt8s/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp8YPt8s/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmprtPal0/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp8YPt8s/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp8YPt8s/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    Setting:
     options(
     spades.outputPath = '/tmp/RtmpC8Csq2/simOutputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmprtPal0/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp8YPt8s/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpC8Csq2/simOutputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    --- finished re-building ‘ii-modules.Rmd’
    
    Warning: elapsed-time limit of 30 minutes reached for sub-process
    --- re-building ‘iii-cache.Rmd’ using rmarkdown
    Loading required package: sp
    
    Attaching package: 'raster'
    
    The following object is masked from 'package:magrittr':
    
     extract
    
    Loading required package: quickPlot
    Loading required package: reproducible
    
    Attaching package: 'SpaDES.core'
    
    The following objects are masked from 'package:stats':
    
     end, start
    
    The following object is masked from 'package:utils':
    
     citation
    
    Setting:
     options(
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmprtPal0/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp8YPt8s/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp8YPt8s/SpaDES/outputs'
     spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    ###### Module Code Checking - Still experimental - please report problems ########
    /data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules/randomLandscapes/randomLandscapes.R
    randomLandscapes: defineParameter: '.useCache' is not of specified type 'logical'.
    randomLandscapes: inputObjects: stackName is used from sim inside doEvent.randomLandscapes, but is not declared in metadata inputObjects
    /data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules/fireSpread/fireSpread.R
    fireSpread: module code: landscape, testStats are declared in metadata inputObjects, but no default(s) are provided in .inputObjects
    fireSpread: inputObjects: stackName, DEM, Fires are used from sim inside doEvent.fireSpread, but are not declared in metadata inputObjects
    ###### Module Code Checking ########
    SUMMARY: processing the following file failed:
     ‘iii-cache.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: quickPlot
    Loading required package: reproducible
    
    Attaching package: 'SpaDES.core'
    
    The following objects are masked from 'package:stats':
    
     end, start
    
    The following object is masked from 'package:utils':
    
     citation
    
    Loading required package: SpaDES.tools
    Loading required package: RandomFields
    Loading required package: sp
    Loading required package: RandomFieldsUtils
    
    Attaching package: 'RandomFields'
    
    The following object is masked from 'package:RandomFieldsUtils':
    
     RFoptions
    
    Setting:
     options(
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/Rtmp3dXEwB/reproducible/cache'
     spades.inputPath = '/tmp/RtmpjUph0g/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpjUph0g/SpaDES/outputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/Rtmp3dXEwB/reproducible/cache'
     spades.inputPath = '/tmp/RtmpjUph0g/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpjUph0g/SpaDES/outputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/Rtmp3dXEwB/reproducible/cache'
     spades.inputPath = '/tmp/RtmpjUph0g/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpjUph0g/SpaDES/outputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/Rtmp3dXEwB/reproducible/cache'
     spades.inputPath = '/tmp/RtmpjUph0g/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpjUph0g/SpaDES/outputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    Setting:
     options(
     spades.outputPath = '/tmp/RtmpRZGeAa/simOutputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/Rtmp3dXEwB/reproducible/cache'
     spades.inputPath = '/tmp/RtmpjUph0g/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpRZGeAa/simOutputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Killed
Flavor: r-patched-linux-x86_64

Version: 0.2.4
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘RandomFields’
Flavor: r-patched-solaris-x86

Version: 0.2.4
Check: tests
Result: ERROR
     Running ‘test-all.R’ [159s/277s]
    Running the tests in ‘tests/test-all.R’ failed.
    Complete output:
     > library(testthat)
     > test_check("SpaDES.core")
     Loading required package: SpaDES.core
     Loading required package: quickPlot
     Loading required package: reproducible
    
     Attaching package: 'SpaDES.core'
    
     The following objects are masked from 'package:stats':
    
     end, start
    
     The following object is masked from 'package:utils':
    
     citation
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 1. Error: test cache (@test-cache.R#32) ────────────────────────────────────
     The 'RandomFields' package is required but not installed.
     1: eval(expr) at testthat/test-cache.R:32
     2: eval(expr)
     3: experiment(Copy(mySim), replicates = 2, cache = TRUE, debug = FALSE, omitArgs = c("progress",
     "debug", ".plotInitialTime", ".saveInitialTime"))
     4: experiment(Copy(mySim), replicates = 2, cache = TRUE, debug = FALSE, omitArgs = c("progress",
     "debug", ".plotInitialTime", ".saveInitialTime"))
     5: do.call(get(parFun), args)
     6: (function (X, FUN, ...)
     {
     FUN <- match.fun(FUN)
     if (!is.vector(X) || is.object(X))
     X <- as.list(X)
     .Internal(lapply(X, FUN))
     })(X = 1:2, FUN = function (ind, ...)
     {
     mod <- strsplit(names(factorialExp), split = "\\.") %>% sapply(function(x) x[1])
     param <- strsplit(names(factorialExp), split = "\\.") %>% sapply(function(x) x[2])
     param[is.na(param)] <- ""
     paramValues <- factorialExp[ind, ]
     whNotExpLevel <- which(colnames(paramValues) != "expLevel")
     if (length(whNotExpLevel) < length(paramValues)) {
     mod <- mod[whNotExpLevel]
     param <- param[whNotExpLevel]
     paramValues <- paramValues[whNotExpLevel]
     }
     whNotRepl <- which(colnames(paramValues) != "replicate")
     if (length(whNotRepl) < length(paramValues)) {
     repl <- paramValues$replicate
     mod <- mod[whNotRepl]
     param <- param[whNotRepl]
     paramValues <- paramValues[whNotRepl]
     }
     notNA <- which(!is.na(paramValues))
     if (length(notNA) < length(mod)) {
     mod <- mod[notNA]
     param <- param[notNA]
     paramValues <- paramValues[notNA]
     }
     sim_ <- Copy(sim)
     experimentDF <- data.frame(module = character(0), param = character(0), val = I(list()),
     modules = character(0), input = data.frame(), object = character(0), expLevel = numeric(0),
     stringsAsFactors = FALSE)
     for (x in seq_along(mod)) {
     if (any(mod != "modules")) {
     y <- factorialExp[ind, names(paramValues)[x]]
     if (!is.na(y) & (mod[x] != "modules")) {
     val <- params[[mod[x]]][[param[[x]]]][[y]]
     params(sim_)[[mod[x]]][[param[[x]]]] <- val
     experimentDF <- rbindlist(l = list(experimentDF, data.frame(module = if (!(mod[x] %in%
     c("input", "object"))) mod[x] else NA, param = if (!(mod[x] %in%
     c("input", "object"))) param[x] else NA, val = if (!(mod[x] %in%
     c("input", "object"))) I(list(val)) else list(NA), modules = paste0(unlist(modules[factorialExp[ind,
     "modules"]]), collapse = ","), input = if (mod[x] %in% c("input")) inputs[[factorialExp[ind,
     "input"]]] else NA, object = if (mod[x] %in% c("object")) names(objects)[[factorialExp[ind,
     "object"]]] else NA, expLevel = factorialExp[ind, "expLevel"],
     stringsAsFactors = FALSE)), use.names = TRUE, fill = TRUE)
     }
     }
     else {
     experimentDF <- rbindlist(l = list(experimentDF, data.frame(modules = paste0(unlist(modules[factorialExp[ind,
     "modules"]]), collapse = ","), expLevel = factorialExp[ind, "expLevel"],
     stringsAsFactors = FALSE)), use.names = TRUE, fill = TRUE)
     }
     if (!any(unlist(lapply(modules, is.null)))) {
     if ("modules" %in% names(factorialExp)) {
     if (!identical(sort(unlist(modules[factorialExp[ind, "modules"]])),
     sort(unlist(SpaDES.core::modules(sim))))) {
     sim_ <- simInit(params = params(sim_), modules = as.list(unlist(modules[factorialExp[ind,
     "modules"]])), times = append(lapply(times(sim_)[2:3], as.numeric),
     times(sim_)[4]), paths = paths(sim_), outputs = outputs(sim_))
     }
     }
     }
     else {
     sim_ <- sim
     }
     }
     if (any(dirPrefix == "simNum")) {
     exptNum <- paddedFloatToChar(factorialExp$expLevel[ind], ceiling(log10(numExpLevels +
     1)))
     }
     dirPrefixTmp <- paste0(dirPrefix, collapse = "")
     if ((numExpLevels > 1) & (substrLength > 0)) {
     dirName <- paste(collapse = "-", substr(mod, 1, substrLength), substr(param,
     1, substrLength), paramValues, sep = "_")
     dirName <- gsub(dirName, pattern = "__", replacement = "_")
     if (any(dirPrefix == "simNum")) {
     dirPrefix <- gsub(dirPrefixTmp, pattern = "simNum", replacement = exptNum)
     }
     if (any(dirPrefix != "")) {
     dirName <- paste(paste(dirPrefix, collapse = ""), dirName, sep = "_")
     }
     }
     else if (substrLength == 0) {
     if (any(dirPrefix != "")) {
     simplePrefix <- if (any(dirPrefix == "simNum"))
     exptNum
     else ""
     dirName <- gsub(dirPrefixTmp, pattern = "simNum", replacement = simplePrefix)
     }
     }
     else {
     if (any(dirPrefix != "")) {
     dirName <- gsub(dirPrefixTmp, pattern = "simNum", replacement = "")
     }
     }
     if (exists("repl", inherits = FALSE)) {
     nn <- paste0("rep", paddedFloatToChar(repl, ceiling(log10(length(replicates) +
     1))))
     dirName <- if (!is.null(dirName)) {
     file.path(dirName, nn)
     }
     else {
     file.path(nn)
     }
     }
     newOutputPath <- file.path(paths(sim_)$outputPath, dirName) %>% gsub(pattern = "/$",
     replacement = "") %>% gsub(pattern = "//", replacement = "/")
     if (!dir.exists(newOutputPath))
     dir.create(newOutputPath, recursive = TRUE)
     paths(sim_)$outputPath <- newOutputPath
     if (NROW(outputs(sim_))) {
     outputs(sim_)$file <- file.path(newOutputPath, basename(outputs(sim_)$file))
     }
     if (length(inputs) > 0) {
     SpaDES.core::inputs(sim_) <- inputs[[factorialExp[ind, "input"]]]
     }
     if (length(objects) > 0) {
     replaceObjName <- strsplit(names(objects)[[factorialExp[ind, "object"]]],
     split = "\\.")[[1]][1]
     sim_[[replaceObjName]] <- objects[[factorialExp[ind, "object"]]]
     }
     dots <- list(...)
     if (is.null(dots$cache))
     dots$cache <- FALSE
     sim3 <- spades(sim_, replicate = ind, ...)
     return(list(sim3, experimentDF))
     }, cache = TRUE, debug = FALSE, omitArgs = c("progress", "debug", ".plotInitialTime",
     ".saveInitialTime"), notOlderThan = NULL)
     7: FUN(X[[i]], ...)
     8: spades(sim_, replicate = ind, ...)
     9: spades(sim_, replicate = ind, ...)
     10: do.call(quote = TRUE, Cache, args = append(list(spades, sim = sim, debug = debug,
     progress = progress, .plotInitialTime = .plotInitialTime, .saveInitialTime = .saveInitialTime,
     omitArgs = omitArgs, notOlderThan = notOlderThan), dots))
     ...
     16: FUN(...)
     17: FUN(...)
     18: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     19: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     20: eval(fnCallAsExpr)
     21: eval(fnCallAsExpr)
     22: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     23: Init(sim)
     24: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     25: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 2. Error: test event-level cache (@test-cache.R#83) ────────────────────────
     The 'RandomFields' package is required but not installed.
     1: expect_true(!"Using cached copy of init event in randomLandscapes module" %in% capture_output(sims <- spades(Copy(mySim),
     notOlderThan = Sys.time(), debug = FALSE))) at testthat/test-cache.R:83
     2: quasi_label(enquo(object), label)
     3: eval_bare(get_expr(quo), get_env(quo))
     4: "Using cached copy of init event in randomLandscapes module" %in% capture_output(sims <- spades(Copy(mySim),
     notOlderThan = Sys.time(), debug = FALSE))
     5: capture_output(sims <- spades(Copy(mySim), notOlderThan = Sys.time(), debug = FALSE))
     6: capture_output_lines(code, print, width = width)
     7: eval_with_output(code, print = print, width = width)
     8: withr::with_output_sink(temp, withVisible(code))
     9: force(code)
     10: withVisible(code)
     ...
     16: eval(fnCallAsExpr)
     17: Cache(FUN = get(moduleCall, envir = fnEnv), sim = sim, eventTime = cur[["eventTime"]],
     eventType = cur[["eventType"]], .objects = moduleSpecificObjects, notOlderThan = notOlderThan,
     outputObjects = moduleSpecificOutputObjects, classOptions = classOptions, cacheRepo = sim@paths[["cachePath"]])
     18: standardGeneric("Cache")
     19: eval(mc, env)
     20: eval(mc, env)
     21: Cache(FUN = FUN, ..., notOlderThan = notOlderThan, .objects = .objects, outputObjects = outputObjects,
     cacheRepo = cacheRepo, classOptions = classOptions)
     22: FUN(...)
     23: Init(sim)
     24: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     25: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 3. Error: test module-level cache (@test-cache.R#131) ──────────────────────
     The 'RandomFields' package is required but not installed.
     1: expect_true(!("Using cached copy of init event in randomLandscapes module" %in% capture_output(sims <- spades(Copy(mySim),
     notOlderThan = Sys.time(), debug = FALSE)))) at testthat/test-cache.R:131
     2: quasi_label(enquo(object), label)
     3: eval_bare(get_expr(quo), get_env(quo))
     4: "Using cached copy of init event in randomLandscapes module" %in% capture_output(sims <- spades(Copy(mySim),
     notOlderThan = Sys.time(), debug = FALSE))
     5: capture_output(sims <- spades(Copy(mySim), notOlderThan = Sys.time(), debug = FALSE))
     6: capture_output_lines(code, print, width = width)
     7: eval_with_output(code, print = print, width = width)
     8: withr::with_output_sink(temp, withVisible(code))
     9: force(code)
     10: withVisible(code)
     ...
     16: eval(fnCallAsExpr)
     17: Cache(FUN = get(moduleCall, envir = fnEnv), sim = sim, eventTime = cur[["eventTime"]],
     eventType = cur[["eventType"]], .objects = moduleSpecificObjects, notOlderThan = notOlderThan,
     outputObjects = moduleSpecificOutputObjects, classOptions = classOptions, cacheRepo = sim@paths[["cachePath"]])
     18: standardGeneric("Cache")
     19: eval(mc, env)
     20: eval(mc, env)
     21: Cache(FUN = FUN, ..., notOlderThan = notOlderThan, .objects = .objects, outputObjects = outputObjects,
     cacheRepo = cacheRepo, classOptions = classOptions)
     22: FUN(...)
     23: Init(sim)
     24: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     25: stop("The 'RandomFields' package is required but not installed.")
    
     Using cached copy of .inputObjects event in test module.
     Failed with error: 'there is no package called 'RandomFields''
     ── 4. Error: test checkpointing (@test-checkpoint.R#24) ───────────────────────
     The 'RandomFields' package is required but not installed.
     1: suppressWarnings(spades(simA)) at testthat/test-checkpoint.R:24
     2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     3: spades(simA)
     4: spades(simA)
     5: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     6: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     7: eval(fnCallAsExpr)
     8: eval(fnCallAsExpr)
     9: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     10: Init(sim)
     11: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     12: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 5. Error: test checkpointing with disk-backed raster (@test-checkpoint.R#85)
     The 'RandomFields' package is required but not installed.
     1: spades(simA) at testthat/test-checkpoint.R:85
     2: spades(simA)
     3: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     4: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     5: eval(fnCallAsExpr)
     6: eval(fnCallAsExpr)
     7: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     8: Init(sim)
     9: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     10: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 6. Error: simulation runs with simInit and spades (@test-conditionalEvents.R#
     The 'RandomFields' package is required but not installed.
     1: spades(mySim, debug = FALSE) at testthat/test-conditionalEvents.R:74
     2: spades(mySim, debug = FALSE)
     3: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     4: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     5: eval(fnCallAsExpr)
     6: eval(fnCallAsExpr)
     7: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     8: Init(sim)
     9: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     10: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 7. Error: experiment does not work correctly (@test-experiment.R#33) ───────
     The 'RandomFields' package is required but not installed.
     1: experiment(mySimFull, params = experimentParams) at testthat/test-experiment.R:33
     2: experiment(mySimFull, params = experimentParams)
     3: do.call(get(parFun), args)
     4: (function (X, FUN, ...)
     {
     FUN <- match.fun(FUN)
     if (!is.vector(X) || is.object(X))
     X <- as.list(X)
     .Internal(lapply(X, FUN))
     })(X = 1:4, FUN = function (ind, ...)
     {
     mod <- strsplit(names(factorialExp), split = "\\.") %>% sapply(function(x) x[1])
     param <- strsplit(names(factorialExp), split = "\\.") %>% sapply(function(x) x[2])
     param[is.na(param)] <- ""
     paramValues <- factorialExp[ind, ]
     whNotExpLevel <- which(colnames(paramValues) != "expLevel")
     if (length(whNotExpLevel) < length(paramValues)) {
     mod <- mod[whNotExpLevel]
     param <- param[whNotExpLevel]
     paramValues <- paramValues[whNotExpLevel]
     }
     whNotRepl <- which(colnames(paramValues) != "replicate")
     if (length(whNotRepl) < length(paramValues)) {
     repl <- paramValues$replicate
     mod <- mod[whNotRepl]
     param <- param[whNotRepl]
     paramValues <- paramValues[whNotRepl]
     }
     notNA <- which(!is.na(paramValues))
     if (length(notNA) < length(mod)) {
     mod <- mod[notNA]
     param <- param[notNA]
     paramValues <- paramValues[notNA]
     }
     sim_ <- Copy(sim)
     experimentDF <- data.frame(module = character(0), param = character(0), val = I(list()),
     modules = character(0), input = data.frame(), object = character(0), expLevel = numeric(0),
     stringsAsFactors = FALSE)
     for (x in seq_along(mod)) {
     if (any(mod != "modules")) {
     y <- factorialExp[ind, names(paramValues)[x]]
     if (!is.na(y) & (mod[x] != "modules")) {
     val <- params[[mod[x]]][[param[[x]]]][[y]]
     params(sim_)[[mod[x]]][[param[[x]]]] <- val
     experimentDF <- rbindlist(l = list(experimentDF, data.frame(module = if (!(mod[x] %in%
     c("input", "object"))) mod[x] else NA, param = if (!(mod[x] %in%
     c("input", "object"))) param[x] else NA, val = if (!(mod[x] %in%
     c("input", "object"))) I(list(val)) else list(NA), modules = paste0(unlist(modules[factorialExp[ind,
     "modules"]]), collapse = ","), input = if (mod[x] %in% c("input")) inputs[[factorialExp[ind,
     "input"]]] else NA, object = if (mod[x] %in% c("object")) names(objects)[[factorialExp[ind,
     "object"]]] else NA, expLevel = factorialExp[ind, "expLevel"],
     stringsAsFactors = FALSE)), use.names = TRUE, fill = TRUE)
     }
     }
     else {
     experimentDF <- rbindlist(l = list(experimentDF, data.frame(modules = paste0(unlist(modules[factorialExp[ind,
     "modules"]]), collapse = ","), expLevel = factorialExp[ind, "expLevel"],
     stringsAsFactors = FALSE)), use.names = TRUE, fill = TRUE)
     }
     if (!any(unlist(lapply(modules, is.null)))) {
     if ("modules" %in% names(factorialExp)) {
     if (!identical(sort(unlist(modules[factorialExp[ind, "modules"]])),
     sort(unlist(SpaDES.core::modules(sim))))) {
     sim_ <- simInit(params = params(sim_), modules = as.list(unlist(modules[factorialExp[ind,
     "modules"]])), times = append(lapply(times(sim_)[2:3], as.numeric),
     times(sim_)[4]), paths = paths(sim_), outputs = outputs(sim_))
     }
     }
     }
     else {
     sim_ <- sim
     }
     }
     if (any(dirPrefix == "simNum")) {
     exptNum <- paddedFloatToChar(factorialExp$expLevel[ind], ceiling(log10(numExpLevels +
     1)))
     }
     dirPrefixTmp <- paste0(dirPrefix, collapse = "")
     if ((numExpLevels > 1) & (substrLength > 0)) {
     dirName <- paste(collapse = "-", substr(mod, 1, substrLength), substr(param,
     1, substrLength), paramValues, sep = "_")
     dirName <- gsub(dirName, pattern = "__", replacement = "_")
     if (any(dirPrefix == "simNum")) {
     dirPrefix <- gsub(dirPrefixTmp, pattern = "simNum", replacement = exptNum)
     }
     if (any(dirPrefix != "")) {
     dirName <- paste(paste(dirPrefix, collapse = ""), dirName, sep = "_")
     }
     }
     else if (substrLength == 0) {
     if (any(dirPrefix != "")) {
     simplePrefix <- if (any(dirPrefix == "simNum"))
     exptNum
     else ""
     dirName <- gsub(dirPrefixTmp, pattern = "simNum", replacement = simplePrefix)
     }
     }
     else {
     if (any(dirPrefix != "")) {
     dirName <- gsub(dirPrefixTmp, pattern = "simNum", replacement = "")
     }
     }
     if (exists("repl", inherits = FALSE)) {
     nn <- paste0("rep", paddedFloatToChar(repl, ceiling(log10(length(replicates) +
     1))))
     dirName <- if (!is.null(dirName)) {
     file.path(dirName, nn)
     }
     else {
     file.path(nn)
     }
     }
     newOutputPath <- file.path(paths(sim_)$outputPath, dirName) %>% gsub(pattern = "/$",
     replacement = "") %>% gsub(pattern = "//", replacement = "/")
     if (!dir.exists(newOutputPath))
     dir.create(newOutputPath, recursive = TRUE)
     paths(sim_)$outputPath <- newOutputPath
     if (NROW(outputs(sim_))) {
     outputs(sim_)$file <- file.path(newOutputPath, basename(outputs(sim_)$file))
     }
     if (length(inputs) > 0) {
     SpaDES.core::inputs(sim_) <- inputs[[factorialExp[ind, "input"]]]
     }
     if (length(objects) > 0) {
     replaceObjName <- strsplit(names(objects)[[factorialExp[ind, "object"]]],
     split = "\\.")[[1]][1]
     sim_[[replaceObjName]] <- objects[[factorialExp[ind, "object"]]]
     }
     dots <- list(...)
     if (is.null(dots$cache))
     dots$cache <- FALSE
     sim3 <- spades(sim_, replicate = ind, ...)
     return(list(sim3, experimentDF))
     }, notOlderThan = NULL)
     5: FUN(X[[i]], ...)
     6: spades(sim_, replicate = ind, ...)
     7: spades(sim_, replicate = ind, ...)
     8: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     9: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     10: eval(fnCallAsExpr)
     11: eval(fnCallAsExpr)
     12: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     13: Init(sim)
     14: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     15: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 8. Error: test-load.R: loading inputs does not work correctly (@test-load.R#3
     The 'RandomFields' package is required but not installed.
     1: spades(mySim) at testthat/test-load.R:36
     2: spades(mySim)
     3: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     4: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     5: eval(fnCallAsExpr)
     6: eval(fnCallAsExpr)
     7: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     8: Init(sim)
     9: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     10: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 9. Error: test-load.R: passing arguments to filelist in simInit does not work
     The 'RandomFields' package is required but not installed.
     1: spades(sim2) at testthat/test-load.R:164
     2: spades(sim2)
     3: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     4: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     5: eval(fnCallAsExpr)
     6: eval(fnCallAsExpr)
     7: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     8: Init(sim)
     9: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     10: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 10. Error: test-load.R: passing objects to simInit does not work correctly (@
     The 'RandomFields' package is required but not installed.
     1: spades(sim6) at testthat/test-load.R:283
     2: spades(sim6)
     3: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     4: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     5: eval(fnCallAsExpr)
     6: eval(fnCallAsExpr)
     7: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     8: Init(sim)
     9: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     10: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 11. Error: simulation runs with simInit and spades (@test-multipleModulePaths
     The 'RandomFields' package is required but not installed.
     1: simInit(times, params, modules = modules, objects = list(), paths) %>% spades(debug = FALSE) at testthat/test-multipleModulePaths.R:77
     2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
     3: eval(quote(`_fseq`(`_lhs`)), env, env)
     4: eval(quote(`_fseq`(`_lhs`)), env, env)
     5: `_fseq`(`_lhs`)
     6: freduce(value, `_function_list`)
     7: withVisible(function_list[[k]](value))
     8: function_list[[k]](value)
     9: spades(., debug = FALSE)
     10: spades(., debug = FALSE)
     11: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     12: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     13: eval(fnCallAsExpr)
     14: eval(fnCallAsExpr)
     15: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     16: Init(sim)
     17: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     18: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 12. Error: test objectSynonyms (@test-objectSynonyms.R#34) ─────────────────
     The 'RandomFields' package is required but not installed.
     1: spades(sim, .plotInitialTime = NA, debug = FALSE) at testthat/test-objectSynonyms.R:34
     2: spades(sim, .plotInitialTime = NA, debug = FALSE)
     3: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     4: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     5: eval(fnCallAsExpr)
     6: eval(fnCallAsExpr)
     7: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     8: Init(sim)
     9: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     10: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 13. Error: saving files does not work correctly (@test-save.R#30) ──────────
     The 'RandomFields' package is required but not installed.
     1: spades(mySim) at testthat/test-save.R:30
     2: spades(mySim)
     3: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     4: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     5: eval(fnCallAsExpr)
     6: eval(fnCallAsExpr)
     7: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     8: Init(sim)
     9: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     10: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 14. Error: simList object initializes correctly (@test-simList.R#302) ──────
     The 'RandomFields' package is required but not installed.
     1: SpaDES.tools::gaussMap(ras, scale = 100, var = 0.01) at testthat/test-simList.R:302
     2: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 15. Error: simulation runs with simInit and spades (@test-simulation.R#19) ─
     The 'RandomFields' package is required but not installed.
     1: simInit(times, params, modules, objects = list(), paths) %>% spades(debug = FALSE) at testthat/test-simulation.R:19
     2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
     3: eval(quote(`_fseq`(`_lhs`)), env, env)
     4: eval(quote(`_fseq`(`_lhs`)), env, env)
     5: `_fseq`(`_lhs`)
     6: freduce(value, `_function_list`)
     7: withVisible(function_list[[k]](value))
     8: function_list[[k]](value)
     9: spades(., debug = FALSE)
     10: spades(., debug = FALSE)
     11: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     12: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     13: eval(fnCallAsExpr)
     14: eval(fnCallAsExpr)
     15: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     16: Init(sim)
     17: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     18: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 16. Error: spades calls with different signatures don't work (@test-simulatio
     The 'RandomFields' package is required but not installed.
     1: assign(paste0("st", i), system.time(spades(a, cache = TRUE, .plotInitialTime = NA))) at testthat/test-simulation.R:145
     2: system.time(spades(a, cache = TRUE, .plotInitialTime = NA))
     3: spades(a, cache = TRUE, .plotInitialTime = NA)
     4: spades(a, cache = TRUE, .plotInitialTime = NA)
     5: do.call(quote = TRUE, Cache, args = append(list(spades, sim = sim, debug = debug,
     progress = progress, .plotInitialTime = .plotInitialTime, .saveInitialTime = .saveInitialTime,
     omitArgs = omitArgs, notOlderThan = notOlderThan), dots))
     6: (new("standardGeneric", .Data = function (FUN, ..., notOlderThan = NULL, .objects = NULL,
     outputObjects = NULL, algo = "xxhash64", cacheRepo = NULL, length = getOption("reproducible.length",
     Inf), compareRasterFileLength, userTags = c(), digestPathContent, omitArgs = NULL,
     classOptions = list(), debugCache = character(), sideEffect = FALSE, makeCopy = FALSE,
     quick = getOption("reproducible.quick", FALSE), verbose = getOption("reproducible.verbose",
     0), cacheId = NULL, useCache = getOption("reproducible.useCache", TRUE),
     showSimilar = NULL)
     standardGeneric("Cache"), generic = structure("Cache", package = "reproducible"),
     package = "reproducible", group = list(), valueClass = character(0), signature = "...",
     default = new("derivedDefaultMethod", .Data = function (FUN, ..., notOlderThan = NULL,
     .objects = NULL, outputObjects = NULL, algo = "xxhash64", cacheRepo = NULL,
     length = getOption("reproducible.length", Inf), compareRasterFileLength,
     userTags = c(), digestPathContent, omitArgs = NULL, classOptions = list(),
     debugCache = character(), sideEffect = FALSE, makeCopy = FALSE, quick = getOption("reproducible.quick",
     FALSE), verbose = getOption("reproducible.verbose", 0), cacheId = NULL,
     useCache = getOption("reproducible.useCache", TRUE), showSimilar = NULL)
     {
     archivist::cache(cacheRepo, FUN, ..., notOlderThan, algo, userTags = userTags)
     }, target = new("signature", .Data = "ANY", names = "FUN", package = "methods"),
     defined = new("signature", .Data = "ANY", names = "FUN", package = "methods"),
     generic = structure("Cache", package = "reproducible")), skeleton = (new("derivedDefaultMethod",
     .Data = function (FUN, ..., notOlderThan = NULL, .objects = NULL, outputObjects = NULL,
     algo = "xxhash64", cacheRepo = NULL, length = getOption("reproducible.length",
     Inf), compareRasterFileLength, userTags = c(), digestPathContent,
     omitArgs = NULL, classOptions = list(), debugCache = character(), sideEffect = FALSE,
     makeCopy = FALSE, quick = getOption("reproducible.quick", FALSE), verbose = getOption("reproducible.verbose",
     0), cacheId = NULL, useCache = getOption("reproducible.useCache",
     TRUE), showSimilar = NULL)
     {
     archivist::cache(cacheRepo, FUN, ..., notOlderThan, algo, userTags = userTags)
     }, target = new("signature", .Data = "ANY", names = "FUN", package = "methods"),
     defined = new("signature", .Data = "ANY", names = "FUN", package = "methods"),
     generic = structure("Cache", package = "reproducible")))(FUN, ..., notOlderThan = notOlderThan,
     .objects = .objects, outputObjects = outputObjects, algo = algo, cacheRepo = cacheRepo,
     length = length, compareRasterFileLength = compareRasterFileLength, userTags = userTags,
     digestPathContent = digestPathContent, omitArgs = omitArgs, classOptions = classOptions,
     debugCache = debugCache, sideEffect = sideEffect, makeCopy = makeCopy, quick = quick,
     verbose = verbose, cacheId = cacheId, useCache = useCache, showSimilar = showSimilar)))(quote(new("nonstandardGenericFunction",
     .Data = function (sim, debug = getOption("spades.debug"), progress = NA, cache,
     .plotInitialTime = NULL, .saveInitialTime = NULL, notOlderThan = NULL, ...)
     {
     standardGeneric("spades")
     }, generic = structure("spades", package = "SpaDES.core"), package = "SpaDES.core",
     group = list(), valueClass = character(0), signature = c("sim", "debug", "progress",
     "cache", ".plotInitialTime", ".saveInitialTime", "notOlderThan"), default = NULL,
     skeleton = (function (sim, debug = getOption("spades.debug"), progress = NA,
     cache, .plotInitialTime = NULL, .saveInitialTime = NULL, notOlderThan = NULL,
     ...)
     stop("invalid call in method dispatch to 'spades' (no default method)", domain = NA))(sim,
     debug, progress, cache, .plotInitialTime, .saveInitialTime, notOlderThan,
     ...))), sim = quote(new("simList", modules = structure(list("checkpoint",
     "save", "progress", "load", `/home/ripley/R/Lib32/SpaDES.core/sampleModules/randomLandscapes` = "randomLandscapes",
     `/home/ripley/R/Lib32/SpaDES.core/sampleModules/fireSpread` = "fireSpread"), modulesGraph = structure(list(
     from = character(0), to = character(0)), row.names = integer(0), class = "data.frame")),
     params = list(.checkpoint = list(file = NULL, interval = NA_real_), .progress = list(
     interval = NA_real_, type = NA_character_), .globals = list(burnStats = "npixelsburned",
     stackName = "landscape"), randomLandscapes = list(.plotInitialTime = structure(0, unit = "year"),
     .plotInterval = NA_real_, .saveInitialTime = NA_real_, .saveInterval = NA_real_,
     .useCache = FALSE, inRAM = FALSE, nx = 20, ny = 20, stackName = "landscape"),
     fireSpread = list(.plotInitialTime = structure(0, unit = "year"), .plotInterval = 1,
     .saveInitialTime = NA_real_, .saveInterval = NA_real_, its = 1e+06, nFires = 10L,
     persistprob = 0, returnInterval = 1, spreadprob = 0.225, stackName = "landscape",
     startTime = structure(1, unit = "year"))), events = list(list(eventTime = structure(0, unit = "second"),
     moduleName = "checkpoint", eventType = "init", eventPriority = 5), list(eventTime = structure(0, unit = "second"),
     moduleName = "save", eventType = "init", eventPriority = 5), list(eventTime = structure(0, unit = "second"),
     moduleName = "progress", eventType = "init", eventPriority = 5), list(eventTime = structure(0, unit = "second"),
     moduleName = "load", eventType = "init", eventPriority = 5), list(eventTime = structure(0, unit = "second"),
     moduleName = "randomLandscapes", eventType = "init", eventPriority = 5),
     list(eventTime = structure(0, unit = "second"), moduleName = "fireSpread",
     eventType = "init", eventPriority = 5)), current = list(), completed = list(),
     depends = new(".simDeps", dependencies = list(randomLandscapes = new(".moduleDeps",
     name = "randomLandscapes", description = "Generate RasterStack of random maps representative of a forest landscape (DEM, forestAge, forestCover, habitatQuality, percentPine). Requires a global simulation parameter `stackName` be set.",
     keywords = c("random map", "random landscape"), childModules = character(0),
     authors = structure(list(list(given = c("Alex", "M"), family = "Chubaty",
     role = c("aut", "cre"), email = "alexander.chubaty@canada.ca", comment = NULL),
     list(given = c("Eliot", "J", "B"), family = "McIntire", role = c("aut",
     "cre"), email = "eliot.mcintire@canada.ca", comment = NULL)), class = "person"),
     version = structure(list(c(1L, 6L, 0L)), class = "numeric_version"), spatialExtent = new("Extent",
     xmin = NA_real_, xmax = NA_real_, ymin = NA_real_, ymax = NA_real_),
     timeframe = structure(list(sec = c(NA_real_, NA_real_), min = c(NA_integer_,
     NA_integer_), hour = c(NA_integer_, NA_integer_), mday = c(NA_integer_, NA_integer_
     ), mon = c(NA_integer_, NA_integer_), year = c(NA_integer_, NA_integer_),
     wday = c(NA_integer_, NA_integer_), yday = c(NA_integer_, NA_integer_
     ), isdst = c(-1L, -1L), zone = c("", ""), gmtoff = c(NA_integer_, NA_integer_
     )), class = c("POSIXlt", "POSIXt"), tzone = c("GB", "GMT", "BST")), timeunit = "year",
     citation = list(), documentation = list(), reqdPkgs = list("raster", "RColorBrewer",
     "SpaDES.tools"), parameters = structure(list(paramName = c("inRAM", "nx",
     "ny", "stackName", ".plotInitialTime", ".plotInterval", ".saveInitialTime",
     ".saveInterval", ".useCache"), paramClass = c("logical", "numeric", "numeric",
     "character", "numeric", "numeric", "numeric", "numeric", "logical"), default = structure(list(
     FALSE, 100L, 100L, "landscape", structure(0, unit = "year"), NA_real_,
     NA_real_, NA_real_, FALSE), class = "AsIs"), min = structure(list(TRUE,
     10L, 10L, NA, structure(0, unit = "year"), NA, NA, NA, c("init", "plot"
     )), class = "AsIs"), max = structure(list(FALSE, 500L, 500L, NA, NA,
     NA, NA, NA, NA), class = "AsIs"), paramDesc = c("should the raster be stored in memory?",
     "size of map (number of pixels) in the x dimension", "size of map (number of pixels) in the y dimension",
     "name of the RasterStack", "time to schedule first plot event", "time interval between plot events",
     "time to schedule first save event", "time interval between save events",
     "should the module result be cached for future use")), row.names = c(NA,
     -9L), class = "data.frame"), inputObjects = structure(list(objectName = NA_character_,
     objectClass = NA_character_, desc = NA_character_, sourceURL = NA_character_,
     other = list(NA_character_)), class = "data.frame", row.names = c(NA,
     -1L)), outputObjects = structure(list(objectName = "landscape", objectClass = "RasterStack",
     desc = NA_character_, other = list(NA_character_)), class = "data.frame", row.names = c(NA,
     -1L))), fireSpread = new(".moduleDeps", name = "fireSpread", description = "Simulate fire ignition and spread on a landscape, where spread probability varies according to percent pine. Fire size statistics are collected immediately after each burn event. Requires a global simulation parameter `stackName` be set.",
     keywords = c("fire", "percolation model", "spread algorithm"), childModules = character(0),
     authors = structure(list(list(given = c("Alex", "M"), family = "Chubaty",
     role = c("aut", "cre"), email = "alexander.chubaty@canada.ca", comment = NULL),
     list(given = c("Eliot", "J", "B"), family = "McIntire", role = c("aut",
     "cre"), email = "eliot.mcintire@canada.ca", comment = NULL), list(given = "Steve",
     family = "Cumming", role = "aut", email = "Steve.Cumming@sbf.ulaval.ca",
     comment = NULL)), class = "person"), version = structure(list(c(1L,
     6L, 0L)), class = "numeric_version"), spatialExtent = new("Extent", xmin = NA_real_,
     xmax = NA_real_, ymin = NA_real_, ymax = NA_real_), timeframe = structure(list(
     sec = c(NA_real_, NA_real_), min = c(NA_integer_, NA_integer_), hour = c(NA_integer_,
     NA_integer_), mday = c(NA_integer_, NA_integer_), mon = c(NA_integer_,
     NA_integer_), year = c(NA_integer_, NA_integer_), wday = c(NA_integer_,
     NA_integer_), yday = c(NA_integer_, NA_integer_), isdst = c(-1L, -1L),
     zone = c("", ""), gmtoff = c(NA_integer_, NA_integer_)), class = c("POSIXlt",
     "POSIXt"), tzone = c("GB", "GMT", "BST")), timeunit = "year", citation = list(),
     documentation = list(), reqdPkgs = list("methods", "raster", "RColorBrewer",
     "SpaDES.tools"), parameters = structure(list(paramName = c("stackName",
     "nFires", "its", "persistprob", "returnInterval", "spreadprob", "startTime",
     ".plotInitialTime", ".plotInterval", ".saveInitialTime", ".saveInterval"),
     paramClass = c("character", "numeric", "numeric", "numeric", "numeric",
     "numeric", "numeric", "numeric", "numeric", "numeric", "numeric"), default = structure(list(
     "landscape", 10L, 1e+06, 0, 1, 0.225, structure(1, unit = "year"),
     structure(0, unit = "year"), 1, NA_real_, NA_real_), class = "AsIs"),
     min = structure(list(NA, 1L, 1e+06, 0, 1, 0.05, 0, structure(0, unit = "year"),
     1, NA, NA), class = "AsIs"), max = structure(list(NA, 100L, 1e+06,
     1, 1, 0.5, structure(0, unit = "year"), structure(1, unit = "year"),
     1, NA, NA), class = "AsIs"), paramDesc = c("name of the RasterStack",
     "number of fires to initiate", "number of iterations for fire spread",
     "probability of fire persisting in a pixel", "fire return interval",
     "probability of fire spreading into a pixel", "time of initial fire ignition",
     "time to schedule first plot event", "time interval between plot events",
     "time to schedule first save event", "time interval between save events"
     )), row.names = c(NA, -11L), class = "data.frame"), inputObjects = structure(list(
     objectName = c("landscape", "npixelsburned"), objectClass = c("RasterStack",
     "numeric"), desc = c(NA_character_, NA_character_), sourceURL = c(NA_character_,
     NA_character_)), class = "data.frame", row.names = c(NA, -2L)), outputObjects = structure(list(
     objectName = c("landscape", "npixelsburned"), objectClass = c("RasterStack",
     "numeric"), desc = c(NA_character_, NA_character_), other = list(NA_character_,
     NA_character_)), class = "data.frame", row.names = c(NA, -2L))))),
     simtimes = list(current = structure(0, unit = "second"), start = structure(0, unit = "second"),
     end = structure(0, unit = "second"), timeunit = "year"), inputs = structure(list(
     file = character(0), fun = character(0), package = character(0), objectName = character(0),
     loadTime = numeric(0), loaded = logical(0), arguments = structure(list(), class = "AsIs"),
     intervals = numeric(0)), class = "data.frame", row.names = integer(0)), outputs = structure(list(
     file = character(0), fun = character(0), package = character(0), objectName = character(0),
     saveTime = numeric(0), saved = logical(0), arguments = structure(list(), class = "AsIs")), class = "data.frame", row.names = integer(0)),
     paths = list(cachePath = "/tmp/RtmpZEaa0J/cache", inputPath = "/tmp/RtmpZEaa0J/oMpSW2",
     modulePath = "/home/ripley/R/Lib32/SpaDES.core/sampleModules", outputPath = "/tmp/RtmpZEaa0J/oMpSW2"),
     .envir = <environment>, .xData = <environment>)), debug = quote(FALSE), progress = quote(NA),
     .plotInitialTime = quote(NA), .saveInitialTime = quote(NULL), omitArgs = quote("notOlderThan"),
     notOlderThan = quote(NULL))
     7: standardGeneric("Cache")
     8: eval(mc, env)
     9: eval(mc, env)
     10: Cache(FUN = FUN, ..., notOlderThan = notOlderThan, omitArgs = omitArgs)
     11: FUN(...)
     12: FUN(...)
     13: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     14: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     15: eval(fnCallAsExpr)
     16: eval(fnCallAsExpr)
     17: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     18: Init(sim)
     19: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     20: stop("The 'RandomFields' package is required but not installed.")
    
     Failed with error: 'there is no package called 'RandomFields''
     ── 17. Error: simInitAndSpades (@test-simulation.R#867) ───────────────────────
     The 'RandomFields' package is required but not installed.
     1: simInitAndSpades(times = times, params = params, modules = modules, objects = list(),
     paths = paths, debug = FALSE) at testthat/test-simulation.R:867
     2: do.call(spades, objsSpades)
     3: (new("nonstandardGenericFunction", .Data = function (sim, debug = getOption("spades.debug"),
     progress = NA, cache, .plotInitialTime = NULL, .saveInitialTime = NULL, notOlderThan = NULL,
     ...)
     {
     standardGeneric("spades")
     }, generic = structure("spades", package = "SpaDES.core"), package = "SpaDES.core",
     group = list(), valueClass = character(0), signature = c("sim", "debug", "progress",
     "cache", ".plotInitialTime", ".saveInitialTime", "notOlderThan"), default = NULL,
     skeleton = (function (sim, debug = getOption("spades.debug"), progress = NA,
     cache, .plotInitialTime = NULL, .saveInitialTime = NULL, notOlderThan = NULL,
     ...)
     stop("invalid call in method dispatch to 'spades' (no default method)", domain = NA))(sim,
     debug, progress, cache, .plotInitialTime, .saveInitialTime, notOlderThan,
     ...)))(sim = sim, debug = FALSE, progress = , cache = , .plotInitialTime = ,
     .saveInitialTime = , notOlderThan = )
     4: (new("nonstandardGenericFunction", .Data = function (sim, debug = getOption("spades.debug"),
     progress = NA, cache, .plotInitialTime = NULL, .saveInitialTime = NULL, notOlderThan = NULL,
     ...)
     {
     standardGeneric("spades")
     }, generic = structure("spades", package = "SpaDES.core"), package = "SpaDES.core",
     group = list(), valueClass = character(0), signature = c("sim", "debug", "progress",
     "cache", ".plotInitialTime", ".saveInitialTime", "notOlderThan"), default = NULL,
     skeleton = (function (sim, debug = getOption("spades.debug"), progress = NA,
     cache, .plotInitialTime = NULL, .saveInitialTime = NULL, notOlderThan = NULL,
     ...)
     stop("invalid call in method dispatch to 'spades' (no default method)", domain = NA))(sim,
     debug, progress, cache, .plotInitialTime, .saveInitialTime, notOlderThan,
     ...)))(sim = sim, debug = FALSE, progress = , cache = , .plotInitialTime = ,
     .saveInitialTime = , notOlderThan = )
     5: doEvent(sim, debug = debug, notOlderThan = notOlderThan)
     6: .runEvent(sim, cacheIt, debug, moduleCall, fnEnv, cur, notOlderThan)
     7: eval(fnCallAsExpr)
     8: eval(fnCallAsExpr)
     9: get(moduleCall, envir = fnEnv)(sim, cur[["eventTime"]], cur[["eventType"]])
     10: Init(sim)
     11: gaussMap(template, scale = 300, var = 0.03, speedup = speedup, inMemory = inMemory)
     12: stop("The 'RandomFields' package is required but not installed.")
    
     Using cached copy of .inputObjects event in child6 module.
     Using memoised copy of .inputObjects event in child6 module
     Using memoised copy of .inputObjects event in child6 module
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 336 SKIPPED: 32 FAILED: 17
     1. Error: test cache (@test-cache.R#32)
     2. Error: test event-level cache (@test-cache.R#83)
     3. Error: test module-level cache (@test-cache.R#131)
     4. Error: test checkpointing (@test-checkpoint.R#24)
     5. Error: test checkpointing with disk-backed raster (@test-checkpoint.R#85)
     6. Error: simulation runs with simInit and spades (@test-conditionalEvents.R#74)
     7. Error: experiment does not work correctly (@test-experiment.R#33)
     8. Error: test-load.R: loading inputs does not work correctly (@test-load.R#36)
     9. Error: test-load.R: passing arguments to filelist in simInit does not work correctly (@test-load.R#164)
     1. ...
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: quickPlot
    Loading required package: reproducible
    
    Attaching package: 'SpaDES.core'
    
    The following objects are masked from 'package:stats':
    
     end, start
    
    The following object is masked from 'package:utils':
    
     citation
    
    Loading required package: SpaDES.tools
    Loading required package: RandomFields
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'RandomFields'
    Setting:
     options(
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpHKaWlJ/reproducible/cache'
     spades.inputPath = '/tmp/RtmpM.aO9G/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpM.aO9G/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Quitting from lines 476-499 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    there is no package called 'webshot'
    Execution halted
Flavor: r-patched-solaris-x86

Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
    Attaching package: 'igraph'
    
    The following objects are masked from 'package:stats':
    
     decompose, spectrum
    
    The following object is masked from 'package:base':
    
     union
    
    Loading required package: quickPlot
    Loading required package: reproducible
    
    Attaching package: 'SpaDES.core'
    
    The following objects are masked from 'package:stats':
    
     end, start
    
    The following object is masked from 'package:utils':
    
     citation
    
    Loading required package: SpaDES.tools
    Loading required package: RandomFields
    Loading required package: sp
    Loading required package: RandomFieldsUtils
    
    Attaching package: 'RandomFields'
    
    The following object is masked from 'package:RandomFieldsUtils':
    
     RFoptions
    
    Setting:
     options(
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpSqKked/reproducible/cache'
     spades.inputPath = '/tmp/Rtmpd2MEfn/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpd2MEfn/SpaDES/outputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpSqKked/reproducible/cache'
     spades.inputPath = '/tmp/Rtmpd2MEfn/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpd2MEfn/SpaDES/outputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpSqKked/reproducible/cache'
     spades.inputPath = '/tmp/Rtmpd2MEfn/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpd2MEfn/SpaDES/outputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Setting:
     options(
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpSqKked/reproducible/cache'
     spades.inputPath = '/tmp/Rtmpd2MEfn/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpd2MEfn/SpaDES/outputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    
    Attaching package: 'data.table'
    
    The following object is masked from 'package:raster':
    
     shift
    
    Setting:
     options(
     spades.outputPath = '/tmp/RtmpL3pB1g/simOutputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpSqKked/reproducible/cache'
     spades.inputPath = '/tmp/Rtmpd2MEfn/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpL3pB1g/simOutputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Killed
Flavor: r-release-linux-x86_64

Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    The following object is masked from 'package:RandomFieldsUtils':
    
     RFoptions
    
    The following objects are masked from 'package:base':
    
     abs, acosh, asin, asinh, atan, atan2, atanh, cos, cosh, exp,
     expm1, floor, gamma, lgamma, log, log1p, log2, logb, max, min,
     round, sin, sinh, sqrt, tan, tanh, trunc
    
    Setting:
     options(
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/private/tmp/RtmpblkGAL/reproducible/cache'
     spades.inputPath = '/private/tmp/RtmpP9tEJ9/SpaDES/inputs'
     spades.outputPath = '/private/tmp/RtmpP9tEJ9/SpaDES/outputs'
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Quitting from lines 376-382 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.2.4
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    The following object is masked from 'package:RandomFieldsUtils':
    
     RFoptions
    
    The following objects are masked from 'package:base':
    
     abs, acosh, asin, asinh, atan, atan2, atanh, cos, cosh, exp,
     expm1, floor, gamma, lgamma, log, log1p, log2, logb, max, min,
     round, sin, sinh, sqrt, tan, tanh, trunc
    
    Setting:
     options(
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/private/tmp/RtmpAQt4Kz/reproducible/cache'
     spades.inputPath = '/private/tmp/RtmpFl5Sri/SpaDES/inputs'
     spades.outputPath = '/private/tmp/RtmpFl5Sri/SpaDES/outputs'
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Quitting from lines 376-382 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    cannot open the connection
    Execution halted
Flavor: r-oldrel-osx-x86_64