CRAN Package Check Results for Package SpaDES.core

Last updated on 2020-09-23 08:08:43 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.3 45.54 425.20 470.74 OK
r-devel-linux-x86_64-debian-gcc 1.0.3 38.09 337.23 375.32 OK
r-devel-linux-x86_64-fedora-clang 1.0.3 586.52 OK
r-devel-linux-x86_64-fedora-gcc 1.0.3 563.13 OK
r-devel-windows-ix86+x86_64 1.0.3 83.00 485.00 568.00 OK
r-patched-linux-x86_64 1.0.3 45.88 404.92 450.80 OK
r-patched-solaris-x86 1.0.3 807.60 WARN
r-release-linux-x86_64 1.0.3 41.72 409.21 450.93 OK
r-release-macos-x86_64 1.0.3 ERROR
r-release-windows-ix86+x86_64 1.0.3 85.00 477.00 562.00 OK
r-oldrel-macos-x86_64 1.0.3 WARN
r-oldrel-windows-ix86+x86_64 1.0.3 57.00 333.00 390.00 OK

Check Details

Version: 1.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘i-introduction.Rmd’ using rmarkdown
    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.
    --- finished re-building ‘i-introduction.Rmd’
    
    --- re-building ‘ii-modules.Rmd’ using rmarkdown
    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(
     rasterTmpDir = '/tmp/Rtmp_HaqXT/working_dir/Rtmp9Caqc5/raster'
     reproducible.cachePath = '/tmp/Rtmp_HaqXT/working_dir/Rtmp9Caqc5/Require/cache'
     spades.inputPath = '/tmp/RtmpG0aG_a/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpG0aG_a/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Loading required package: RColorBrewer
    Loading required package: raster
    2020-09-22 23:34:17 INFO:: total elpsd: 0.0056 secs | 0 checkpoint init 0
    2020-09-22 23:34:17 INFO:: total elpsd: 0.79 secs | 0 save init 0
    2020-09-22 23:34:17 INFO:: total elpsd: 0.79 secs | 0 progress init 0
    2020-09-22 23:34:17 INFO:: total elpsd: 0.8 secs | 0 load init 0
    2020-09-22 23:34:17 INFO:: total elpsd: 0.81 secs | 0 randomLandscapes init
    2020-09-22 23:34:22 INFO:: total elpsd: 5.7 secs | 0 fireSpread init 1
    2020-09-22 23:34:22 INFO:: total elpsd: 5.8 secs | 0 caribouMovement init 1
    2020-09-22 23:34:22 INFO:: total elpsd: 5.8 secs | 0 fireSpread burn 5
    2020-09-22 23:34:23 INFO:: total elpsd: 6.2 secs | 0 fireSpread stats 5
    2020-09-22 23:34:23 INFO:: total elpsd: 6.3 secs | 0 randomLandscapes plot 1
    2020-09-22 23:34:23 INFO:: total elpsd: 6.8 secs | 0 fireSpread plot.init 10
    2020-09-22 23:34:24 INFO:: total elpsd: 7.1 secs | 0.08333 caribouMovement p
    2020-09-22 23:34:24 INFO:: total elpsd: 7.4 secs | 0.1667 caribouMovement pl
    2020-09-22 23:34:24 INFO:: total elpsd: 7.6 secs | 0.25 caribouMovement plot
    2020-09-22 23:34:24 INFO:: total elpsd: 7.8 secs | 0.3333 caribouMovement pl
    2020-09-22 23:34:24 INFO:: total elpsd: 7.9 secs | 0.4167 caribouMovement pl
    2020-09-22 23:34:25 INFO:: total elpsd: 8.1 secs | 0.5 caribouMovement plot
    2020-09-22 23:34:25 INFO:: total elpsd: 8.3 secs | 0.5833 caribouMovement pl
    2020-09-22 23:34:25 INFO:: total elpsd: 8.5 secs | 0.6667 caribouMovement pl
    2020-09-22 23:34:25 INFO:: total elpsd: 8.7 secs | 0.75 caribouMovement plot
    2020-09-22 23:34:25 INFO:: total elpsd: 8.9 secs | 0.8333 caribouMovement pl
    2020-09-22 23:34:26 INFO:: total elpsd: 9 secs | 0.9167 caribouMovement plot
    2020-09-22 23:34:26 INFO:: total elpsd: 9.2 secs | 1 caribouMovement move 5
    2020-09-22 23:34:26 INFO:: total elpsd: 9.3 secs | 1 fireSpread burn 5
    2020-09-22 23:34:27 INFO:: total elpsd: 11 secs | 1 fireSpread stats 5
    2020-09-22 23:34:27 INFO:: total elpsd: 11 secs | 1 caribouMovement plot 10
    2020-09-22 23:34:28 INFO:: total elpsd: 11 secs | 1.083 caribouMovement move
    2020-09-22 23:34:28 INFO:: total elpsd: 11 secs | 1.083 caribouMovement plot
    2020-09-22 23:34:28 INFO:: total elpsd: 11 secs | 1.167 caribouMovement move
    2020-09-22 23:34:28 INFO:: total elpsd: 11 secs | 1.167 caribouMovement plot
    2020-09-22 23:34:28 INFO:: total elpsd: 12 secs | 1.25 caribouMovement move
    2020-09-22 23:34:28 INFO:: total elpsd: 12 secs | 1.25 caribouMovement plot
    2020-09-22 23:34:28 INFO:: total elpsd: 12 secs | 1.333 caribouMovement move
    2020-09-22 23:34:28 INFO:: total elpsd: 12 secs | 1.333 caribouMovement plot
    2020-09-22 23:34:29 INFO:: total elpsd: 12 secs | 1.417 caribouMovement move
    2020-09-22 23:34:29 INFO:: total elpsd: 12 secs | 1.417 caribouMovement plot
    2020-09-22 23:34:29 INFO:: total elpsd: 12 secs | 1.5 caribouMovement move 5
    2020-09-22 23:34:29 INFO:: total elpsd: 12 secs | 1.5 caribouMovement plot 1
    2020-09-22 23:34:29 INFO:: total elpsd: 13 secs | 1.583 caribouMovement move
    2020-09-22 23:34:29 INFO:: total elpsd: 13 secs | 1.583 caribouMovement plot
    2020-09-22 23:34:29 INFO:: total elpsd: 13 secs | 1.667 caribouMovement move
    2020-09-22 23:34:29 INFO:: total elpsd: 13 secs | 1.667 caribouMovement plot
    2020-09-22 23:34:29 INFO:: total elpsd: 13 secs | 1.75 caribouMovement move
    2020-09-22 23:34:29 INFO:: total elpsd: 13 secs | 1.75 caribouMovement plot
    2020-09-22 23:34:30 INFO:: total elpsd: 13 secs | 1.833 caribouMovement move
    2020-09-22 23:34:30 INFO:: total elpsd: 13 secs | 1.833 caribouMovement plot
    2020-09-22 23:34:30 INFO:: total elpsd: 13 secs | 1.917 caribouMovement move
    2020-09-22 23:34:30 INFO:: total elpsd: 13 secs | 1.917 caribouMovement plot
    2020-09-22 23:34:30 INFO:: total elpsd: 14 secs | 2 fireSpread burn 5
    2020-09-22 23:34:30 INFO:: total elpsd: 14 secs | 2 caribouMovement move 5
    2020-09-22 23:34:30 INFO:: total elpsd: 14 secs | 2 fireSpread stats 5
    2020-09-22 23:34:30 INFO:: total elpsd: 14 secs | 2 caribouMovement plot 10
    simList saved in
     SpaDES.core:::.pkgEnv$.sim
    It will be deleted at next spades() call.
    Quitting from lines 386-390 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    there is no package called 'webshot'
    --- failed re-building ‘ii-modules.Rmd’
    
    --- re-building ‘iii-cache.Rmd’ using rmarkdown
    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.
    Loading required package: sp
    
    Attaching package: 'raster'
    
    The following object is masked from 'package:magrittr':
    
     extract
    
    Loading required package: quickPlot
    
    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 = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/tmp/Rtmp_HaqXT/working_dir/Rtmpoiay.f/raster'
     reproducible.cachePath = '/tmp/Rtmp_HaqXT/working_dir/Rtmpoiay.f/Require/cache'
     spades.inputPath = '/tmp/RtmpG0aG_a/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpG0aG_a/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Loading required package: RColorBrewer
    Loading required package: SpaDES.tools
    --- finished re-building ‘iii-cache.Rmd’
    
    --- re-building ‘iv-advanced.Rmd’ using rmarkdown
    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.
    --- finished re-building ‘iv-advanced.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.0.3
Check: tests
Result: ERROR
     Running ‘test-all.R’ [64s/69s]
    Running the tests in ‘tests/test-all.R’ failed.
    Last 13 lines of output:
     Backtrace:
     1. testthat::expect_true(any(grepl("grandpar1", communities(mg$communities)[["1"]])))
     5. igraph::communities(mg$communities)
     6. igraph::membership(x)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 508 | SKIPPED: 18 | WARNINGS: 2 | FAILED: 5 ]
     1. Failure: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#215)
     2. Failure: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#216)
     3. Failure: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#217)
     4. Failure: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#218)
     5. Error: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#219)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-release-macos-x86_64

Version: 1.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘i-introduction.Rmd’ using rmarkdown
    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.
    --- finished re-building ‘i-introduction.Rmd’
    
    --- re-building ‘ii-modules.Rmd’ using rmarkdown
    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 = '/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/Volumes/Temp/tmp/RtmpsFtBYf/raster'
     reproducible.cachePath = '/Volumes/Temp/tmp/RtmpsFtBYf/Require/cache'
     spades.inputPath = '/Volumes/Temp/tmp/RtmpsQ9YgY/SpaDES/inputs'
     spades.outputPath = '/Volumes/Temp/tmp/RtmpsQ9YgY/SpaDES/outputs'
     spades.modulePath = '/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Loading required package: RColorBrewer
    Loading required package: raster
    2020-09-21 06:58:08 INFO:: total elpsd: 0.0015 secs | 0 checkpoint init 0
    2020-09-21 06:58:08 INFO:: total elpsd: 0.14 secs | 0 save init 0
    2020-09-21 06:58:08 INFO:: total elpsd: 0.15 secs | 0 progress init 0
    2020-09-21 06:58:08 INFO:: total elpsd: 0.15 secs | 0 load init 0
    2020-09-21 06:58:08 INFO:: total elpsd: 0.15 secs | 0 randomLandscapes init
    2020-09-21 06:58:09 INFO:: total elpsd: 0.92 secs | 0 fireSpread init 1
    2020-09-21 06:58:09 INFO:: total elpsd: 0.94 secs | 0 caribouMovement init 1
    2020-09-21 06:58:09 INFO:: total elpsd: 0.96 secs | 0 fireSpread burn 5
    2020-09-21 06:58:09 INFO:: total elpsd: 1 secs | 0 fireSpread stats 5
    2020-09-21 06:58:09 INFO:: total elpsd: 1 secs | 0 randomLandscapes plot 10
    2020-09-21 06:58:09 INFO:: total elpsd: 1.1 secs | 0 fireSpread plot.init 10
    2020-09-21 06:58:09 INFO:: total elpsd: 1.2 secs | 0.08333 caribouMovement p
    2020-09-21 06:58:09 INFO:: total elpsd: 1.3 secs | 0.1667 caribouMovement pl
    2020-09-21 06:58:09 INFO:: total elpsd: 1.3 secs | 0.25 caribouMovement plot
    2020-09-21 06:58:09 INFO:: total elpsd: 1.4 secs | 0.3333 caribouMovement pl
    2020-09-21 06:58:09 INFO:: total elpsd: 1.4 secs | 0.4167 caribouMovement pl
    2020-09-21 06:58:10 INFO:: total elpsd: 1.5 secs | 0.5 caribouMovement plot
    2020-09-21 06:58:10 INFO:: total elpsd: 1.5 secs | 0.5833 caribouMovement pl
    2020-09-21 06:58:10 INFO:: total elpsd: 1.6 secs | 0.6667 caribouMovement pl
    2020-09-21 06:58:10 INFO:: total elpsd: 1.7 secs | 0.75 caribouMovement plot
    2020-09-21 06:58:10 INFO:: total elpsd: 1.7 secs | 0.8333 caribouMovement pl
    2020-09-21 06:58:10 INFO:: total elpsd: 1.8 secs | 0.9167 caribouMovement pl
    2020-09-21 06:58:10 INFO:: total elpsd: 1.8 secs | 1 caribouMovement move 5
    2020-09-21 06:58:10 INFO:: total elpsd: 1.9 secs | 1 fireSpread burn 5
    2020-09-21 06:58:10 INFO:: total elpsd: 2.2 secs | 1 fireSpread stats 5
    2020-09-21 06:58:10 INFO:: total elpsd: 2.2 secs | 1 caribouMovement plot 10
    2020-09-21 06:58:10 INFO:: total elpsd: 2.3 secs | 1.083 caribouMovement mov
    2020-09-21 06:58:10 INFO:: total elpsd: 2.3 secs | 1.083 caribouMovement plo
    2020-09-21 06:58:10 INFO:: total elpsd: 2.4 secs | 1.167 caribouMovement mov
    2020-09-21 06:58:10 INFO:: total elpsd: 2.4 secs | 1.167 caribouMovement plo
    2020-09-21 06:58:10 INFO:: total elpsd: 2.4 secs | 1.25 caribouMovement move
    2020-09-21 06:58:10 INFO:: total elpsd: 2.5 secs | 1.25 caribouMovement plot
    2020-09-21 06:58:11 INFO:: total elpsd: 2.5 secs | 1.333 caribouMovement mov
    2020-09-21 06:58:11 INFO:: total elpsd: 2.5 secs | 1.333 caribouMovement plo
    2020-09-21 06:58:11 INFO:: total elpsd: 2.6 secs | 1.417 caribouMovement mov
    2020-09-21 06:58:11 INFO:: total elpsd: 2.6 secs | 1.417 caribouMovement plo
    2020-09-21 06:58:11 INFO:: total elpsd: 2.6 secs | 1.5 caribouMovement move
    2020-09-21 06:58:11 INFO:: total elpsd: 2.6 secs | 1.5 caribouMovement plot
    2020-09-21 06:58:11 INFO:: total elpsd: 2.7 secs | 1.583 caribouMovement mov
    2020-09-21 06:58:11 INFO:: total elpsd: 2.7 secs | 1.583 caribouMovement plo
    2020-09-21 06:58:11 INFO:: total elpsd: 2.8 secs | 1.667 caribouMovement mov
    2020-09-21 06:58:11 INFO:: total elpsd: 2.8 secs | 1.667 caribouMovement plo
    2020-09-21 06:58:11 INFO:: total elpsd: 2.8 secs | 1.75 caribouMovement move
    2020-09-21 06:58:11 INFO:: total elpsd: 2.9 secs | 1.75 caribouMovement plot
    2020-09-21 06:58:11 INFO:: total elpsd: 2.9 secs | 1.833 caribouMovement mov
    2020-09-21 06:58:11 INFO:: total elpsd: 2.9 secs | 1.833 caribouMovement plo
    2020-09-21 06:58:11 INFO:: total elpsd: 3 secs | 1.917 caribouMovement move
    2020-09-21 06:58:11 INFO:: total elpsd: 3 secs | 1.917 caribouMovement plot
    2020-09-21 06:58:11 INFO:: total elpsd: 3 secs | 2 fireSpread burn 5
    2020-09-21 06:58:11 INFO:: total elpsd: 3.1 secs | 2 caribouMovement move 5
    2020-09-21 06:58:11 INFO:: total elpsd: 3.1 secs | 2 fireSpread stats 5
    2020-09-21 06:58:11 INFO:: total elpsd: 3.1 secs | 2 caribouMovement plot 10
    simList saved in
     SpaDES.core:::.pkgEnv$.sim
    It will be deleted at next spades() call.
    Quitting from lines 386-390 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘ii-modules.Rmd’
    
    --- re-building ‘iii-cache.Rmd’ using rmarkdown
    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.
    Loading required package: sp
    
    Attaching package: 'raster'
    
    The following object is masked from 'package:magrittr':
    
     extract
    
    Loading required package: quickPlot
    
    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 = '/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/Volumes/Temp/tmp/RtmpjSlp4O/raster'
     reproducible.cachePath = '/Volumes/Temp/tmp/RtmpjSlp4O/Require/cache'
     spades.inputPath = '/Volumes/Temp/tmp/RtmpsQ9YgY/SpaDES/inputs'
     spades.outputPath = '/Volumes/Temp/tmp/RtmpsQ9YgY/SpaDES/outputs'
     spades.modulePath = '/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Loading required package: RColorBrewer
    Loading required package: SpaDES.tools
    --- finished re-building ‘iii-cache.Rmd’
    
    --- re-building ‘iv-advanced.Rmd’ using rmarkdown
    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.
    --- finished re-building ‘iv-advanced.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 1.0.3
Check: dependencies in R code
Result: NOTE
    No protocol specified
    No protocol specified
Flavor: r-oldrel-macos-x86_64

Version: 1.0.3
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘i-introduction.Rmd’ using rmarkdown
    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.
    --- finished re-building ‘i-introduction.Rmd’
    
    --- re-building ‘ii-modules.Rmd’ using rmarkdown
    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 = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/private/tmp/RtmpifS0II/raster'
     reproducible.cachePath = '/private/tmp/RtmpifS0II/Require/cache'
     spades.inputPath = '/private/tmp/Rtmp6n1B7F/SpaDES/inputs'
     spades.outputPath = '/private/tmp/Rtmp6n1B7F/SpaDES/outputs'
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Loading required package: RColorBrewer
    Loading required package: raster
    2020-09-13 04:56:32 INFO:: total elpsd: 0.0023 secs | 0 checkpoint init 0
    2020-09-13 04:56:33 INFO:: total elpsd: 0.39 secs | 0 save init 0
    2020-09-13 04:56:33 INFO:: total elpsd: 0.39 secs | 0 progress init 0
    2020-09-13 04:56:33 INFO:: total elpsd: 0.39 secs | 0 load init 0
    2020-09-13 04:56:33 INFO:: total elpsd: 0.4 secs | 0 randomLandscapes init 1
    2020-09-13 04:56:34 INFO:: total elpsd: 2.1 secs | 0 fireSpread init 1
    2020-09-13 04:56:34 INFO:: total elpsd: 2.2 secs | 0 caribouMovement init 1
    2020-09-13 04:56:35 INFO:: total elpsd: 2.2 secs | 0 fireSpread burn 5
    2020-09-13 04:56:35 INFO:: total elpsd: 2.3 secs | 0 fireSpread stats 5
    2020-09-13 04:56:35 INFO:: total elpsd: 2.3 secs | 0 randomLandscapes plot 1
    2020-09-13 04:56:35 INFO:: total elpsd: 2.5 secs | 0 fireSpread plot.init 10
    2020-09-13 04:56:35 INFO:: total elpsd: 2.7 secs | 0.08333 caribouMovement p
    2020-09-13 04:56:35 INFO:: total elpsd: 2.8 secs | 0.1667 caribouMovement pl
    2020-09-13 04:56:35 INFO:: total elpsd: 2.9 secs | 0.25 caribouMovement plot
    2020-09-13 04:56:35 INFO:: total elpsd: 3.1 secs | 0.3333 caribouMovement pl
    2020-09-13 04:56:36 INFO:: total elpsd: 3.2 secs | 0.4167 caribouMovement pl
    2020-09-13 04:56:36 INFO:: total elpsd: 3.3 secs | 0.5 caribouMovement plot
    2020-09-13 04:56:36 INFO:: total elpsd: 3.5 secs | 0.5833 caribouMovement pl
    2020-09-13 04:56:36 INFO:: total elpsd: 3.6 secs | 0.6667 caribouMovement pl
    2020-09-13 04:56:36 INFO:: total elpsd: 3.7 secs | 0.75 caribouMovement plot
    2020-09-13 04:56:36 INFO:: total elpsd: 3.9 secs | 0.8333 caribouMovement pl
    2020-09-13 04:56:36 INFO:: total elpsd: 4 secs | 0.9167 caribouMovement plot
    2020-09-13 04:56:36 INFO:: total elpsd: 4.1 secs | 1 caribouMovement move 5
    2020-09-13 04:56:36 INFO:: total elpsd: 4.2 secs | 1 fireSpread burn 5
    2020-09-13 04:56:37 INFO:: total elpsd: 5 secs | 1 fireSpread stats 5
    2020-09-13 04:56:37 INFO:: total elpsd: 5 secs | 1 caribouMovement plot 10
    2020-09-13 04:56:37 INFO:: total elpsd: 5.1 secs | 1.083 caribouMovement mov
    2020-09-13 04:56:37 INFO:: total elpsd: 5.1 secs | 1.083 caribouMovement plo
    2020-09-13 04:56:38 INFO:: total elpsd: 5.3 secs | 1.167 caribouMovement mov
    2020-09-13 04:56:38 INFO:: total elpsd: 5.3 secs | 1.167 caribouMovement plo
    2020-09-13 04:56:38 INFO:: total elpsd: 5.4 secs | 1.25 caribouMovement move
    2020-09-13 04:56:38 INFO:: total elpsd: 5.4 secs | 1.25 caribouMovement plot
    2020-09-13 04:56:38 INFO:: total elpsd: 5.6 secs | 1.333 caribouMovement mov
    2020-09-13 04:56:38 INFO:: total elpsd: 5.6 secs | 1.333 caribouMovement plo
    2020-09-13 04:56:38 INFO:: total elpsd: 5.7 secs | 1.417 caribouMovement mov
    2020-09-13 04:56:38 INFO:: total elpsd: 5.7 secs | 1.417 caribouMovement plo
    2020-09-13 04:56:38 INFO:: total elpsd: 5.9 secs | 1.5 caribouMovement move
    2020-09-13 04:56:38 INFO:: total elpsd: 5.9 secs | 1.5 caribouMovement plot
    2020-09-13 04:56:38 INFO:: total elpsd: 6 secs | 1.583 caribouMovement move
    2020-09-13 04:56:38 INFO:: total elpsd: 6 secs | 1.583 caribouMovement plot
    2020-09-13 04:56:38 INFO:: total elpsd: 6.1 secs | 1.667 caribouMovement mov
    2020-09-13 04:56:38 INFO:: total elpsd: 6.2 secs | 1.667 caribouMovement plo
    2020-09-13 04:56:39 INFO:: total elpsd: 6.3 secs | 1.75 caribouMovement move
    2020-09-13 04:56:39 INFO:: total elpsd: 6.3 secs | 1.75 caribouMovement plot
    2020-09-13 04:56:39 INFO:: total elpsd: 6.4 secs | 1.833 caribouMovement mov
    2020-09-13 04:56:39 INFO:: total elpsd: 6.4 secs | 1.833 caribouMovement plo
    2020-09-13 04:56:39 INFO:: total elpsd: 6.6 secs | 1.917 caribouMovement mov
    2020-09-13 04:56:39 INFO:: total elpsd: 6.6 secs | 1.917 caribouMovement plo
    2020-09-13 04:56:39 INFO:: total elpsd: 6.7 secs | 2 fireSpread burn 5
    2020-09-13 04:56:39 INFO:: total elpsd: 6.8 secs | 2 caribouMovement move 5
    2020-09-13 04:56:39 INFO:: total elpsd: 6.8 secs | 2 fireSpread stats 5
    2020-09-13 04:56:39 INFO:: total elpsd: 6.8 secs | 2 caribouMovement plot 10
    simList saved in
     SpaDES.core:::.pkgEnv$.sim
    It will be deleted at next spades() call.
    Quitting from lines 386-390 (ii-modules.Rmd)
    Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
    cannot open the connection
    --- failed re-building ‘ii-modules.Rmd’
    
    --- re-building ‘iii-cache.Rmd’ using rmarkdown
    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.
    Loading required package: sp
    
    Attaching package: 'raster'
    
    The following object is masked from 'package:magrittr':
    
     extract
    
    Loading required package: quickPlot
    
    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 = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Paths set to:
     options(
     rasterTmpDir = '/private/tmp/Rtmpn36SIZ/raster'
     reproducible.cachePath = '/private/tmp/Rtmpn36SIZ/Require/cache'
     spades.inputPath = '/private/tmp/Rtmp6n1B7F/SpaDES/inputs'
     spades.outputPath = '/private/tmp/Rtmp6n1B7F/SpaDES/outputs'
     spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
     )
    Loading required package: RColorBrewer
    Loading required package: SpaDES.tools
    --- finished re-building ‘iii-cache.Rmd’
    
    --- re-building ‘iv-advanced.Rmd’ using rmarkdown
    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.
    --- finished re-building ‘iv-advanced.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64