CRAN Package Check Results for Package SpaDES.core

Last updated on 2021-01-25 00:48:11 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.5 37.11 320.87 357.98 OK
r-devel-linux-x86_64-debian-gcc 1.0.5 30.97 240.72 271.69 OK
r-devel-linux-x86_64-fedora-clang 1.0.5 425.29 OK
r-devel-linux-x86_64-fedora-gcc 1.0.5 422.08 OK
r-devel-windows-ix86+x86_64 1.0.5 73.00 358.00 431.00 OK
r-patched-linux-x86_64 1.0.5 34.46 303.97 338.43 OK
r-patched-solaris-x86 1.0.5 563.10 WARN
r-release-linux-x86_64 1.0.5 34.46 306.21 340.67 OK
r-release-macos-x86_64 1.0.5 ERROR
r-release-windows-ix86+x86_64 1.0.5 74.00 380.00 454.00 OK
r-oldrel-macos-x86_64 1.0.5 WARN
r-oldrel-windows-ix86+x86_64 1.0.5 54.00 337.00 391.00 OK

Additional issues

M1mac

Check Details

Version: 1.0.5
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/RtmpWnaaF2/working_dir/Rtmp9yaGQN/raster'
     reproducible.cachePath = '/tmp/RtmpWnaaF2/working_dir/Rtmp9yaGQN/Require/cache'
     spades.inputPath = '/tmp/RtmpNpaOQE/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpNpaOQE/SpaDES/outputs'
     spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
     )
    Loading required package: RColorBrewer
    Loading required package: raster
    2021-01-24 11:09:39 INFO:: total elpsd: 0.03 secs | 0 checkpoint init 0
    2021-01-24 11:09:39 INFO:: total elpsd: 0.046 secs | 0 save init 0
    2021-01-24 11:09:39 INFO:: total elpsd: 0.055 secs | 0 progress init 0
    2021-01-24 11:09:39 INFO:: total elpsd: 0.064 secs | 0 load init 0
    2021-01-24 11:09:39 INFO:: total elpsd: 0.072 secs | 0 randomLandscapes init
    2021-01-24 11:09:41 INFO:: total elpsd: 1.6 secs | 0 fireSpread init 1
    2021-01-24 11:09:41 INFO:: total elpsd: 1.6 secs | 0 caribouMovement init 1
    2021-01-24 11:09:41 INFO:: total elpsd: 1.7 secs | 0 fireSpread burn 5
    2021-01-24 11:09:41 INFO:: total elpsd: 1.9 secs | 0 fireSpread stats 5
    2021-01-24 11:09:41 INFO:: total elpsd: 1.9 secs | 0 randomLandscapes plot 1
    2021-01-24 11:09:41 INFO:: total elpsd: 2.5 secs | 0 fireSpread plot.init 10
    2021-01-24 11:09:42 INFO:: total elpsd: 2.9 secs | 0.08333 caribouMovement p
    2021-01-24 11:09:42 INFO:: total elpsd: 3.1 secs | 0.1667 caribouMovement pl
    2021-01-24 11:09:42 INFO:: total elpsd: 3.3 secs | 0.25 caribouMovement plot
    2021-01-24 11:09:42 INFO:: total elpsd: 3.5 secs | 0.3333 caribouMovement pl
    2021-01-24 11:09:43 INFO:: total elpsd: 3.7 secs | 0.4167 caribouMovement pl
    2021-01-24 11:09:43 INFO:: total elpsd: 3.9 secs | 0.5 caribouMovement plot
    2021-01-24 11:09:43 INFO:: total elpsd: 4.1 secs | 0.5833 caribouMovement pl
    2021-01-24 11:09:43 INFO:: total elpsd: 4.4 secs | 0.6667 caribouMovement pl
    2021-01-24 11:09:44 INFO:: total elpsd: 4.6 secs | 0.75 caribouMovement plot
    2021-01-24 11:09:44 INFO:: total elpsd: 4.8 secs | 0.8333 caribouMovement pl
    2021-01-24 11:09:44 INFO:: total elpsd: 5.1 secs | 0.9167 caribouMovement pl
    2021-01-24 11:09:44 INFO:: total elpsd: 5.3 secs | 1 caribouMovement move 5
    2021-01-24 11:09:44 INFO:: total elpsd: 5.3 secs | 1 fireSpread burn 5
    2021-01-24 11:09:46 INFO:: total elpsd: 7.2 secs | 1 fireSpread stats 5
    2021-01-24 11:09:46 INFO:: total elpsd: 7.2 secs | 1 caribouMovement plot 10
    2021-01-24 11:09:46 INFO:: total elpsd: 7.4 secs | 1.083 caribouMovement mov
    2021-01-24 11:09:46 INFO:: total elpsd: 7.5 secs | 1.083 caribouMovement plo
    2021-01-24 11:09:47 INFO:: total elpsd: 7.7 secs | 1.167 caribouMovement mov
    2021-01-24 11:09:47 INFO:: total elpsd: 7.7 secs | 1.167 caribouMovement plo
    2021-01-24 11:09:47 INFO:: total elpsd: 7.9 secs | 1.25 caribouMovement move
    2021-01-24 11:09:47 INFO:: total elpsd: 7.9 secs | 1.25 caribouMovement plot
    2021-01-24 11:09:47 INFO:: total elpsd: 8.1 secs | 1.333 caribouMovement mov
    2021-01-24 11:09:47 INFO:: total elpsd: 8.1 secs | 1.333 caribouMovement plo
    2021-01-24 11:09:47 INFO:: total elpsd: 8.4 secs | 1.417 caribouMovement mov
    2021-01-24 11:09:47 INFO:: total elpsd: 8.4 secs | 1.417 caribouMovement plo
    2021-01-24 11:09:48 INFO:: total elpsd: 8.6 secs | 1.5 caribouMovement move
    2021-01-24 11:09:48 INFO:: total elpsd: 8.6 secs | 1.5 caribouMovement plot
    2021-01-24 11:09:48 INFO:: total elpsd: 8.9 secs | 1.583 caribouMovement mov
    2021-01-24 11:09:48 INFO:: total elpsd: 8.9 secs | 1.583 caribouMovement plo
    2021-01-24 11:09:48 INFO:: total elpsd: 9.1 secs | 1.667 caribouMovement mov
    2021-01-24 11:09:48 INFO:: total elpsd: 9.1 secs | 1.667 caribouMovement plo
    2021-01-24 11:09:48 INFO:: total elpsd: 9.4 secs | 1.75 caribouMovement move
    2021-01-24 11:09:48 INFO:: total elpsd: 9.4 secs | 1.75 caribouMovement plot
    2021-01-24 11:09:49 INFO:: total elpsd: 9.6 secs | 1.833 caribouMovement mov
    2021-01-24 11:09:49 INFO:: total elpsd: 9.7 secs | 1.833 caribouMovement plo
    2021-01-24 11:09:49 INFO:: total elpsd: 9.9 secs | 1.917 caribouMovement mov
    2021-01-24 11:09:49 INFO:: total elpsd: 9.9 secs | 1.917 caribouMovement plo
    2021-01-24 11:09:49 INFO:: total elpsd: 10 secs | 2 fireSpread burn 5
    2021-01-24 11:09:49 INFO:: total elpsd: 10 secs | 2 caribouMovement move 5
    2021-01-24 11:09:49 INFO:: total elpsd: 10 secs | 2 fireSpread stats 5
    2021-01-24 11:09:49 INFO:: total elpsd: 10 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/RtmpWnaaF2/working_dir/RtmpZJa4gS/raster'
     reproducible.cachePath = '/tmp/RtmpWnaaF2/working_dir/RtmpZJa4gS/Require/cache'
     spades.inputPath = '/tmp/RtmpNpaOQE/SpaDES/inputs'
     spades.outputPath = '/tmp/RtmpNpaOQE/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’
    
    --- re-building ‘v-automated-testing.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 ‘v-automated-testing.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.0.5
Check: tests
Result: ERROR
     Running ‘test-all.R’ [31s/32s]
    Running the tests in ‘tests/test-all.R’ failed.
    Last 13 lines of output:
     `expected`: TRUE
     ── Error (test-module-deps-methods.R:219:5): 3 levels of parent and child modules load and show correctly ──
     Error: Cannot calculate community membership
     Backtrace:
     █
     1. ├─testthat::expect_true(any(grepl("grandpar1", communities(mg$communities)[["1"]]))) test-module-deps-methods.R:219:4
     2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
     4. ├─base::grepl("grandpar1", communities(mg$communities)[["1"]])
     5. └─igraph::communities(mg$communities)
     6. └─igraph::membership(x)
    
     [ FAIL 5 | WARN 0 | SKIP 19 | PASS 527 ]
     Error: Test failures
     Execution halted
Flavor: r-release-macos-x86_64

Version: 1.0.5
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/Rtmp8fNB1Z/raster'
     reproducible.cachePath = '/Volumes/Temp/tmp/Rtmp8fNB1Z/Require/cache'
     spades.inputPath = '/Volumes/Temp/tmp/RtmpAOlLsq/SpaDES/inputs'
     spades.outputPath = '/Volumes/Temp/tmp/RtmpAOlLsq/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
    2021-01-23 07:24:46 INFO:: total elpsd: 0.003 secs | 0 checkpoint init 0
    2021-01-23 07:24:46 INFO:: total elpsd: 0.0081 secs | 0 save init 0
    2021-01-23 07:24:46 INFO:: total elpsd: 0.011 secs | 0 progress init 0
    2021-01-23 07:24:46 INFO:: total elpsd: 0.014 secs | 0 load init 0
    2021-01-23 07:24:46 INFO:: total elpsd: 0.017 secs | 0 randomLandscapes init
    2021-01-23 07:24:47 INFO:: total elpsd: 0.28 secs | 0 fireSpread init 1
    2021-01-23 07:24:47 INFO:: total elpsd: 0.29 secs | 0 caribouMovement init 1
    2021-01-23 07:24:47 INFO:: total elpsd: 0.3 secs | 0 fireSpread burn 5
    2021-01-23 07:24:47 INFO:: total elpsd: 0.37 secs | 0 fireSpread stats 5
    2021-01-23 07:24:47 INFO:: total elpsd: 0.38 secs | 0 randomLandscapes plot
    2021-01-23 07:24:47 INFO:: total elpsd: 0.49 secs | 0 fireSpread plot.init 1
    2021-01-23 07:24:47 INFO:: total elpsd: 0.63 secs | 0.08333 caribouMovement
    2021-01-23 07:24:47 INFO:: total elpsd: 0.69 secs | 0.1667 caribouMovement p
    2021-01-23 07:24:47 INFO:: total elpsd: 0.75 secs | 0.25 caribouMovement plo
    2021-01-23 07:24:47 INFO:: total elpsd: 0.81 secs | 0.3333 caribouMovement p
    2021-01-23 07:24:47 INFO:: total elpsd: 0.87 secs | 0.4167 caribouMovement p
    2021-01-23 07:24:47 INFO:: total elpsd: 0.93 secs | 0.5 caribouMovement plot
    2021-01-23 07:24:47 INFO:: total elpsd: 0.99 secs | 0.5833 caribouMovement p
    2021-01-23 07:24:47 INFO:: total elpsd: 1.1 secs | 0.6667 caribouMovement pl
    2021-01-23 07:24:48 INFO:: total elpsd: 1.1 secs | 0.75 caribouMovement plot
    2021-01-23 07:24:48 INFO:: total elpsd: 1.2 secs | 0.8333 caribouMovement pl
    2021-01-23 07:24:48 INFO:: total elpsd: 1.2 secs | 0.9167 caribouMovement pl
    2021-01-23 07:24:48 INFO:: total elpsd: 1.3 secs | 1 caribouMovement move 5
    2021-01-23 07:24:48 INFO:: total elpsd: 1.3 secs | 1 fireSpread burn 5
    2021-01-23 07:24:48 INFO:: total elpsd: 1.7 secs | 1 fireSpread stats 5
    2021-01-23 07:24:48 INFO:: total elpsd: 1.7 secs | 1 caribouMovement plot 10
    2021-01-23 07:24:48 INFO:: total elpsd: 1.8 secs | 1.083 caribouMovement mov
    2021-01-23 07:24:48 INFO:: total elpsd: 1.8 secs | 1.083 caribouMovement plo
    2021-01-23 07:24:48 INFO:: total elpsd: 1.8 secs | 1.167 caribouMovement mov
    2021-01-23 07:24:48 INFO:: total elpsd: 1.8 secs | 1.167 caribouMovement plo
    2021-01-23 07:24:48 INFO:: total elpsd: 1.9 secs | 1.25 caribouMovement move
    2021-01-23 07:24:48 INFO:: total elpsd: 1.9 secs | 1.25 caribouMovement plot
    2021-01-23 07:24:48 INFO:: total elpsd: 2 secs | 1.333 caribouMovement move
    2021-01-23 07:24:48 INFO:: total elpsd: 2 secs | 1.333 caribouMovement plot
    2021-01-23 07:24:48 INFO:: total elpsd: 2 secs | 1.417 caribouMovement move
    2021-01-23 07:24:48 INFO:: total elpsd: 2 secs | 1.417 caribouMovement plot
    2021-01-23 07:24:49 INFO:: total elpsd: 2.1 secs | 1.5 caribouMovement move
    2021-01-23 07:24:49 INFO:: total elpsd: 2.1 secs | 1.5 caribouMovement plot
    2021-01-23 07:24:49 INFO:: total elpsd: 2.2 secs | 1.583 caribouMovement mov
    2021-01-23 07:24:49 INFO:: total elpsd: 2.2 secs | 1.583 caribouMovement plo
    2021-01-23 07:24:49 INFO:: total elpsd: 2.2 secs | 1.667 caribouMovement mov
    2021-01-23 07:24:49 INFO:: total elpsd: 2.3 secs | 1.667 caribouMovement plo
    2021-01-23 07:24:49 INFO:: total elpsd: 2.3 secs | 1.75 caribouMovement move
    2021-01-23 07:24:49 INFO:: total elpsd: 2.3 secs | 1.75 caribouMovement plot
    2021-01-23 07:24:49 INFO:: total elpsd: 2.4 secs | 1.833 caribouMovement mov
    2021-01-23 07:24:49 INFO:: total elpsd: 2.4 secs | 1.833 caribouMovement plo
    2021-01-23 07:24:49 INFO:: total elpsd: 2.4 secs | 1.917 caribouMovement mov
    2021-01-23 07:24:49 INFO:: total elpsd: 2.5 secs | 1.917 caribouMovement plo
    2021-01-23 07:24:49 INFO:: total elpsd: 2.5 secs | 2 fireSpread burn 5
    2021-01-23 07:24:49 INFO:: total elpsd: 2.5 secs | 2 caribouMovement move 5
    2021-01-23 07:24:49 INFO:: total elpsd: 2.5 secs | 2 fireSpread stats 5
    2021-01-23 07:24:49 INFO:: total elpsd: 2.5 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/Rtmpo3CiXU/raster'
     reproducible.cachePath = '/Volumes/Temp/tmp/Rtmpo3CiXU/Require/cache'
     spades.inputPath = '/Volumes/Temp/tmp/RtmpAOlLsq/SpaDES/inputs'
     spades.outputPath = '/Volumes/Temp/tmp/RtmpAOlLsq/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’
    
    --- re-building ‘v-automated-testing.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 ‘v-automated-testing.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 1.0.5
Check: dependencies in R code
Result: NOTE
    No protocol specified
    No protocol specified
Flavor: r-oldrel-macos-x86_64

Version: 1.0.5
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/RtmpxKb9gg/raster'
     reproducible.cachePath = '/private/tmp/RtmpxKb9gg/Require/cache'
     spades.inputPath = '/private/tmp/RtmpddASaV/SpaDES/inputs'
     spades.outputPath = '/private/tmp/RtmpddASaV/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
    2021-01-08 06:47:58 INFO:: total elpsd: 0.0028 secs | 0 checkpoint init 0
    2021-01-08 06:47:58 INFO:: total elpsd: 0.0082 secs | 0 save init 0
    2021-01-08 06:47:58 INFO:: total elpsd: 0.012 secs | 0 progress init 0
    2021-01-08 06:47:58 INFO:: total elpsd: 0.015 secs | 0 load init 0
    2021-01-08 06:47:58 INFO:: total elpsd: 0.017 secs | 0 randomLandscapes init
    2021-01-08 06:47:59 INFO:: total elpsd: 0.46 secs | 0 fireSpread init 1
    2021-01-08 06:47:59 INFO:: total elpsd: 0.48 secs | 0 caribouMovement init 1
    2021-01-08 06:47:59 INFO:: total elpsd: 0.5 secs | 0 fireSpread burn 5
    2021-01-08 06:47:59 INFO:: total elpsd: 0.61 secs | 0 fireSpread stats 5
    2021-01-08 06:47:59 INFO:: total elpsd: 0.61 secs | 0 randomLandscapes plot
    2021-01-08 06:47:59 INFO:: total elpsd: 0.83 secs | 0 fireSpread plot.init 1
    2021-01-08 06:47:59 INFO:: total elpsd: 1 secs | 0.08333 caribouMovement plo
    2021-01-08 06:47:59 INFO:: total elpsd: 1.1 secs | 0.1667 caribouMovement pl
    2021-01-08 06:47:59 INFO:: total elpsd: 1.3 secs | 0.25 caribouMovement plot
    2021-01-08 06:48:00 INFO:: total elpsd: 1.4 secs | 0.3333 caribouMovement pl
    2021-01-08 06:48:00 INFO:: total elpsd: 1.5 secs | 0.4167 caribouMovement pl
    2021-01-08 06:48:00 INFO:: total elpsd: 1.7 secs | 0.5 caribouMovement plot
    2021-01-08 06:48:00 INFO:: total elpsd: 1.8 secs | 0.5833 caribouMovement pl
    2021-01-08 06:48:00 INFO:: total elpsd: 2 secs | 0.6667 caribouMovement plot
    2021-01-08 06:48:00 INFO:: total elpsd: 2.1 secs | 0.75 caribouMovement plot
    2021-01-08 06:48:00 INFO:: total elpsd: 2.2 secs | 0.8333 caribouMovement pl
    2021-01-08 06:48:00 INFO:: total elpsd: 2.4 secs | 0.9167 caribouMovement pl
    2021-01-08 06:48:01 INFO:: total elpsd: 2.5 secs | 1 caribouMovement move 5
    2021-01-08 06:48:01 INFO:: total elpsd: 2.5 secs | 1 fireSpread burn 5
    2021-01-08 06:48:01 INFO:: total elpsd: 3.4 secs | 1 fireSpread stats 5
    2021-01-08 06:48:01 INFO:: total elpsd: 3.4 secs | 1 caribouMovement plot 10
    2021-01-08 06:48:02 INFO:: total elpsd: 3.5 secs | 1.083 caribouMovement mov
    2021-01-08 06:48:02 INFO:: total elpsd: 3.5 secs | 1.083 caribouMovement plo
    2021-01-08 06:48:02 INFO:: total elpsd: 3.7 secs | 1.167 caribouMovement mov
    2021-01-08 06:48:02 INFO:: total elpsd: 3.7 secs | 1.167 caribouMovement plo
    2021-01-08 06:48:02 INFO:: total elpsd: 3.8 secs | 1.25 caribouMovement move
    2021-01-08 06:48:02 INFO:: total elpsd: 3.8 secs | 1.25 caribouMovement plot
    2021-01-08 06:48:02 INFO:: total elpsd: 4 secs | 1.333 caribouMovement move
    2021-01-08 06:48:02 INFO:: total elpsd: 4 secs | 1.333 caribouMovement plot
    2021-01-08 06:48:02 INFO:: total elpsd: 4.1 secs | 1.417 caribouMovement mov
    2021-01-08 06:48:02 INFO:: total elpsd: 4.1 secs | 1.417 caribouMovement plo
    2021-01-08 06:48:02 INFO:: total elpsd: 4.3 secs | 1.5 caribouMovement move
    2021-01-08 06:48:02 INFO:: total elpsd: 4.3 secs | 1.5 caribouMovement plot
    2021-01-08 06:48:03 INFO:: total elpsd: 4.4 secs | 1.583 caribouMovement mov
    2021-01-08 06:48:03 INFO:: total elpsd: 4.4 secs | 1.583 caribouMovement plo
    2021-01-08 06:48:03 INFO:: total elpsd: 4.6 secs | 1.667 caribouMovement mov
    2021-01-08 06:48:03 INFO:: total elpsd: 4.6 secs | 1.667 caribouMovement plo
    2021-01-08 06:48:03 INFO:: total elpsd: 4.7 secs | 1.75 caribouMovement move
    2021-01-08 06:48:03 INFO:: total elpsd: 4.7 secs | 1.75 caribouMovement plot
    2021-01-08 06:48:03 INFO:: total elpsd: 4.9 secs | 1.833 caribouMovement mov
    2021-01-08 06:48:03 INFO:: total elpsd: 4.9 secs | 1.833 caribouMovement plo
    2021-01-08 06:48:03 INFO:: total elpsd: 5 secs | 1.917 caribouMovement move
    2021-01-08 06:48:03 INFO:: total elpsd: 5 secs | 1.917 caribouMovement plot
    2021-01-08 06:48:03 INFO:: total elpsd: 5.2 secs | 2 fireSpread burn 5
    2021-01-08 06:48:03 INFO:: total elpsd: 5.2 secs | 2 caribouMovement move 5
    2021-01-08 06:48:03 INFO:: total elpsd: 5.2 secs | 2 fireSpread stats 5
    2021-01-08 06:48:03 INFO:: total elpsd: 5.2 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/RtmpLDlmPW/raster'
     reproducible.cachePath = '/private/tmp/RtmpLDlmPW/Require/cache'
     spades.inputPath = '/private/tmp/RtmpddASaV/SpaDES/inputs'
     spades.outputPath = '/private/tmp/RtmpddASaV/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’
    
    --- re-building ‘v-automated-testing.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 ‘v-automated-testing.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘ii-modules.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64