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