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/RtmpEhFwYJ/working_dir/RtmpdeXUFK/reproducible/cache'
    spades.inputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/inputs'
    spades.outputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/outputs'
    spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
simList saved in
 SpaDES.core:::.pkgEnv$.sim 
It will be deleted at next spades call
Setting:
  options(
    spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
Paths set to:
  options(
    reproducible.cachePath = '/tmp/RtmpEhFwYJ/working_dir/RtmpdeXUFK/reproducible/cache'
    spades.inputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/inputs'
    spades.outputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/outputs'
    spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
GLPK not found on this system.
 igraph is used internally and requires a GLPK installation.
It can be installed using, e.g., `apt install libglpk-dev`.
If GLPK is installed you should reinstall igraph from source using:
 `install.packages('igraph', type = 'source')`
 For more info see https://github.com/igraph/rigraph/issues/273.
Setting:
  options(
    spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
Paths set to:
  options(
    reproducible.cachePath = '/tmp/RtmpEhFwYJ/working_dir/RtmpdeXUFK/reproducible/cache'
    spades.inputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/inputs'
    spades.outputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/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/RtmpEhFwYJ/working_dir/RtmpdeXUFK/reproducible/cache'
    spades.inputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/inputs'
    spades.outputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/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/RtmpEhFwYJ/working_dir/RtmpdeXUFK/simOutputs'
    spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
Paths set to:
  options(
    reproducible.cachePath = '/tmp/RtmpEhFwYJ/working_dir/RtmpdeXUFK/reproducible/cache'
    spades.inputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/inputs'
    spades.outputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpdeXUFK/simOutputs'
    spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
simList saved in
 SpaDES.core:::.pkgEnv$.sim 
It will be deleted at next spades call
simList saved in
 SpaDES.core:::.pkgEnv$.sim 
It will be deleted at next spades call
--- finished re-building ‘ii-modules.Rmd’

--- 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/RtmpEhFwYJ/working_dir/RtmpSDSjt2/reproducible/cache'
    spades.inputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/inputs'
    spades.outputPath = '/tmp/RtmpEhFwYJ/working_dir/RtmpcMWIhW/SpaDES/outputs'
    spades.modulePath = '/data/gannet/ripley/R/packages/tests-devel/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
Quitting from lines 205-215 (iii-cache.Rmd) 
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
is.character(repoDir) & length(repoDir) == 1 is not TRUE
--- failed re-building ‘iii-cache.Rmd’

SUMMARY: processing the following file failed:
  ‘iii-cache.Rmd’

Error: Vignette re-building failed.
Execution halted