CRAN Package Check Results for Package SpaDES.core

Last updated on 2019-02-20 13:46:45 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.4 44.65 0.02 44.67 FAIL
r-devel-linux-x86_64-debian-gcc 0.2.4 34.04 0.02 34.06 FAIL
r-devel-linux-x86_64-fedora-clang 0.2.4 2999.20 ERROR
r-devel-linux-x86_64-fedora-gcc 0.2.4 3060.48 ERROR
r-devel-windows-ix86+x86_64 0.2.4 80.00 0.00 80.00 OK
r-patched-linux-x86_64 0.2.4 ERROR
r-patched-solaris-x86 0.2.4 3253.70 ERROR
r-release-linux-x86_64 0.2.4 ERROR
r-release-windows-ix86+x86_64 0.2.4 43.00 0.00 43.00 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/14m]
    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/81m]
    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/Rtmpvme5Rf/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpvme5Rf/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/Rtmpvme5Rf/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpvme5Rf/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/Rtmpvme5Rf/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpvme5Rf/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/Rtmpvme5Rf/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpvme5Rf/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/Rtmpa1E6Wi/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/Rtmpvme5Rf/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpa1E6Wi/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/Rtmpvme5Rf/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpvme5Rf/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/50m]
    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/Rtmpx1sV2x/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpx1sV2x/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/Rtmpx1sV2x/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpx1sV2x/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/Rtmpx1sV2x/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpx1sV2x/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/Rtmpx1sV2x/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpx1sV2x/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/RtmpXyQlZt/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/Rtmpx1sV2x/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpXyQlZt/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/Rtmpx1sV2x/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmpx1sV2x/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/RtmpcLYPoP/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp3BAXZR/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp3BAXZR/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/RtmpcLYPoP/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp3BAXZR/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp3BAXZR/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/RtmpcLYPoP/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp3BAXZR/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp3BAXZR/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/RtmpcLYPoP/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp3BAXZR/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp3BAXZR/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/RtmpRiwtbp/simOutputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpcLYPoP/reproducible/cache'
     spades.inputPath = '/tmp/Rtmp3BAXZR/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpRiwtbp/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: 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
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
    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/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/RtmpHKaWlJ/reproducible/cache'
     spades.inputPath = '/tmp/RtmpI2aa9D/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpI2aa9D/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Quitting from lines 376-382 (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/Rtmp2VXO8J/reproducible/cache'
     spades.inputPath = '/tmp/RtmpMxZm03/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpMxZm03/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/Rtmp2VXO8J/reproducible/cache'
     spades.inputPath = '/tmp/RtmpMxZm03/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpMxZm03/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/Rtmp2VXO8J/reproducible/cache'
     spades.inputPath = '/tmp/RtmpMxZm03/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpMxZm03/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/Rtmp2VXO8J/reproducible/cache'
     spades.inputPath = '/tmp/RtmpMxZm03/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpMxZm03/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/Rtmp9n4P83/simOutputs'
     spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     reproducible.cachePath = '/tmp/Rtmp2VXO8J/reproducible/cache'
     spades.inputPath = '/tmp/RtmpMxZm03/SpaDES/inputs'
     spades.outputPath = '/tmp/Rtmp9n4P83/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