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 |
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