Last updated on 2020-08-07 01:50:00 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 2.71 | 2.71 | ERROR | ||
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 2.10 | 2.10 | ERROR | ||
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 11.97 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 2.93 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.1 | 121.00 | 709.00 | 830.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.1 | 2.68 | 2.68 | ERROR | ||
| r-patched-solaris-x86 | 1.0.1 | 6.00 | ERROR | |||
| r-release-linux-x86_64 | 1.0.1 | 2.73 | 2.73 | ERROR | ||
| r-release-macos-x86_64 | 1.0.1 | ERROR | ||||
| r-release-windows-ix86+x86_64 | 1.0.1 | 75.00 | 540.00 | 615.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.1 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.1 | 54.00 | 457.00 | 511.00 | WARN |
Version: 1.0.1
Check: package dependencies
Result: ERROR
Package required but not available: 'reproducible'
Package suggested but not available for checking: 'SpaDES.tools'
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64
Version: 1.0.1
Check: tests
Result: ERROR
Running 'test-all.R' [328s]
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
-- 1. Failure: test checkpointing with disk-backed raster (@test-checkpoint.R#11
`simA` not equal to `simB`.
Component "caribouMovement": Component "Par": Component ".plotInitialTime": Modes: logical, numeric
Component "caribouMovement": Component "Par": Component ".plotInitialTime": target is logical, current is numeric
Component "randomLandscapes": Component "Par": Component ".plotInitialTime": Modes: logical, numeric
Component "randomLandscapes": Component "Par": Component ".plotInitialTime": target is logical, current is numeric
-- 2. Failure: saveSimList does not work correctly (@test-save.R#199) ---------
all.equal(mySim, sim) isn't true.
== testthat results ===========================================================
[ OK: 523 | SKIPPED: 12 | WARNINGS: 4 | FAILED: 2 ]
1. Failure: test checkpointing with disk-backed raster (@test-checkpoint.R#112)
2. Failure: saveSimList does not work correctly (@test-save.R#199)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 1.0.1
Check: tests
Result: ERROR
Running ‘test-all.R’ [390s/558s]
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: 534 | SKIPPED: 11 | WARNINGS: 4 | FAILED: 5 ]
1. Failure: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#204)
2. Failure: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#205)
3. Failure: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#206)
4. Failure: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#207)
5. Error: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#208)
Error: testthat unit tests failed
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.0.1
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/RtmpKf5VkC/raster'
reproducible.cachePath = '/Volumes/Temp/tmp/RtmpKf5VkC/reproducible/cache'
spades.inputPath = '/Volumes/Temp/tmp/RtmphH9xXD/SpaDES/inputs'
spades.outputPath = '/Volumes/Temp/tmp/RtmphH9xXD/SpaDES/outputs'
spades.modulePath = '/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
)
2020-07-17 07:14:21 INFO:: total elpsd: 0.016 secs | 0 checkpoint init 0
2020-07-17 07:14:21 INFO:: total elpsd: 0.02 secs | 0 save init 0
2020-07-17 07:14:21 INFO:: total elpsd: 0.022 secs | 0 progress init 0
2020-07-17 07:14:21 INFO:: total elpsd: 0.024 secs | 0 load init 0
2020-07-17 07:14:21 INFO:: total elpsd: 0.027 secs | 0 randomLandscapes init 1
2020-07-17 07:14:23 INFO:: total elpsd: 1.4 secs | 0 fireSpread init 1
2020-07-17 07:14:23 INFO:: total elpsd: 1.4 secs | 0 caribouMovement init 1
2020-07-17 07:14:23 INFO:: total elpsd: 1.4 secs | 0 fireSpread burn 5
2020-07-17 07:14:23 INFO:: total elpsd: 1.5 secs | 0 fireSpread stats 5
2020-07-17 07:14:23 INFO:: total elpsd: 1.5 secs | 0 randomLandscapes plot 10
2020-07-17 07:14:23 INFO:: total elpsd: 1.7 secs | 0 fireSpread plot.init 10
2020-07-17 07:14:23 INFO:: total elpsd: 1.8 secs | 0.08333 caribouMovement plot.init 10
2020-07-17 07:14:23 INFO:: total elpsd: 1.9 secs | 0.1667 caribouMovement plot 10
2020-07-17 07:14:23 INFO:: total elpsd: 2 secs | 0.25 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 2.1 secs | 0.3333 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 2.2 secs | 0.4167 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 2.3 secs | 0.5 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 2.5 secs | 0.5833 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 2.6 secs | 0.6667 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 2.7 secs | 0.75 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 2.8 secs | 0.8333 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 2.9 secs | 0.9167 caribouMovement plot 10
2020-07-17 07:14:24 INFO:: total elpsd: 3 secs | 1 caribouMovement move 5
2020-07-17 07:14:24 INFO:: total elpsd: 3.1 secs | 1 fireSpread burn 5
2020-07-17 07:14:25 INFO:: total elpsd: 3.7 secs | 1 fireSpread stats 5
2020-07-17 07:14:25 INFO:: total elpsd: 3.7 secs | 1 caribouMovement plot 10
2020-07-17 07:14:25 INFO:: total elpsd: 3.8 secs | 1.083 caribouMovement move 5
2020-07-17 07:14:25 INFO:: total elpsd: 3.9 secs | 1.083 caribouMovement plot 10
2020-07-17 07:14:25 INFO:: total elpsd: 4 secs | 1.167 caribouMovement move 5
2020-07-17 07:14:25 INFO:: total elpsd: 4 secs | 1.167 caribouMovement plot 10
2020-07-17 07:14:25 INFO:: total elpsd: 4.1 secs | 1.25 caribouMovement move 5
2020-07-17 07:14:25 INFO:: total elpsd: 4.1 secs | 1.25 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 4.2 secs | 1.333 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 4.2 secs | 1.333 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 4.3 secs | 1.417 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 4.3 secs | 1.417 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 4.4 secs | 1.5 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 4.4 secs | 1.5 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 4.5 secs | 1.583 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 4.5 secs | 1.583 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 4.6 secs | 1.667 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 4.6 secs | 1.667 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 4.7 secs | 1.75 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 4.7 secs | 1.75 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 4.8 secs | 1.833 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 4.8 secs | 1.833 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 4.9 secs | 1.917 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 4.9 secs | 1.917 caribouMovement plot 10
2020-07-17 07:14:26 INFO:: total elpsd: 5 secs | 2 fireSpread burn 5
2020-07-17 07:14:26 INFO:: total elpsd: 5 secs | 2 caribouMovement move 5
2020-07-17 07:14:26 INFO:: total elpsd: 5 secs | 2 fireSpread stats 5
2020-07-17 07:14:26 INFO:: total elpsd: 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/RtmpdB38HM/raster'
reproducible.cachePath = '/Volumes/Temp/tmp/RtmpdB38HM/reproducible/cache'
spades.inputPath = '/Volumes/Temp/tmp/RtmphH9xXD/SpaDES/inputs'
spades.outputPath = '/Volumes/Temp/tmp/RtmphH9xXD/SpaDES/outputs'
spades.modulePath = '/Volumes/Builds/packages/high-sierra-x86_64/results/4.0/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
)
--- finished re-building ‘iii-cache.Rmd’
--- re-building ‘iv-advanced.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘iv-advanced.Rmd’
SUMMARY: processing the following file failed:
‘ii-modules.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.0.1
Check: dependencies in R code
Result: NOTE
No protocol specified
No protocol specified
Flavor: r-oldrel-macos-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘i-introduction.Rmd’ using rmarkdown
Warning in engine$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/RtmpRyPa2B/raster'
reproducible.cachePath = '/private/tmp/RtmpRyPa2B/reproducible/cache'
spades.inputPath = '/private/tmp/RtmpXjNkz0/SpaDES/inputs'
spades.outputPath = '/private/tmp/RtmpXjNkz0/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'
)
2020-05-21 04:48:48 INFO:: total elpsd: 0.0028 secs | 0 checkpoint init 0
2020-05-21 04:48:48 INFO:: total elpsd: 0.0082 secs | 0 save init 0
2020-05-21 04:48:48 INFO:: total elpsd: 0.012 secs | 0 progress init 0
2020-05-21 04:48:48 INFO:: total elpsd: 0.015 secs | 0 load init 0
2020-05-21 04:48:48 INFO:: total elpsd: 0.018 secs | 0 randomLandscapes init 1
2020-05-21 04:48:50 INFO:: total elpsd: 1.7 secs | 0 fireSpread init 1
2020-05-21 04:48:50 INFO:: total elpsd: 1.8 secs | 0 caribouMovement init 1
2020-05-21 04:48:50 INFO:: total elpsd: 1.8 secs | 0 fireSpread burn 5
2020-05-21 04:48:50 INFO:: total elpsd: 1.9 secs | 0 fireSpread stats 5
2020-05-21 04:48:50 INFO:: total elpsd: 1.9 secs | 0 randomLandscapes plot 10
2020-05-21 04:48:50 INFO:: total elpsd: 2.1 secs | 0 fireSpread plot.init 10
2020-05-21 04:48:50 INFO:: total elpsd: 2.3 secs | 0.08333 caribouMovement plot.init 10
2020-05-21 04:48:51 INFO:: total elpsd: 2.4 secs | 0.1667 caribouMovement plot 10
2020-05-21 04:48:51 INFO:: total elpsd: 2.5 secs | 0.25 caribouMovement plot 10
2020-05-21 04:48:51 INFO:: total elpsd: 2.7 secs | 0.3333 caribouMovement plot 10
2020-05-21 04:48:51 INFO:: total elpsd: 2.8 secs | 0.4167 caribouMovement plot 10
2020-05-21 04:48:51 INFO:: total elpsd: 3 secs | 0.5 caribouMovement plot 10
2020-05-21 04:48:51 INFO:: total elpsd: 3.1 secs | 0.5833 caribouMovement plot 10
2020-05-21 04:48:51 INFO:: total elpsd: 3.2 secs | 0.6667 caribouMovement plot 10
2020-05-21 04:48:51 INFO:: total elpsd: 3.3 secs | 0.75 caribouMovement plot 10
2020-05-21 04:48:52 INFO:: total elpsd: 3.5 secs | 0.8333 caribouMovement plot 10
2020-05-21 04:48:52 INFO:: total elpsd: 3.6 secs | 0.9167 caribouMovement plot 10
2020-05-21 04:48:52 INFO:: total elpsd: 3.7 secs | 1 caribouMovement move 5
2020-05-21 04:48:52 INFO:: total elpsd: 3.8 secs | 1 fireSpread burn 5
2020-05-21 04:48:53 INFO:: total elpsd: 4.6 secs | 1 fireSpread stats 5
2020-05-21 04:48:53 INFO:: total elpsd: 4.6 secs | 1 caribouMovement plot 10
2020-05-21 04:48:53 INFO:: total elpsd: 4.7 secs | 1.083 caribouMovement move 5
2020-05-21 04:48:53 INFO:: total elpsd: 4.8 secs | 1.083 caribouMovement plot 10
2020-05-21 04:48:53 INFO:: total elpsd: 4.9 secs | 1.167 caribouMovement move 5
2020-05-21 04:48:53 INFO:: total elpsd: 4.9 secs | 1.167 caribouMovement plot 10
2020-05-21 04:48:53 INFO:: total elpsd: 5 secs | 1.25 caribouMovement move 5
2020-05-21 04:48:53 INFO:: total elpsd: 5 secs | 1.25 caribouMovement plot 10
2020-05-21 04:48:53 INFO:: total elpsd: 5.2 secs | 1.333 caribouMovement move 5
2020-05-21 04:48:53 INFO:: total elpsd: 5.2 secs | 1.333 caribouMovement plot 10
2020-05-21 04:48:53 INFO:: total elpsd: 5.3 secs | 1.417 caribouMovement move 5
2020-05-21 04:48:53 INFO:: total elpsd: 5.3 secs | 1.417 caribouMovement plot 10
2020-05-21 04:48:54 INFO:: total elpsd: 5.5 secs | 1.5 caribouMovement move 5
2020-05-21 04:48:54 INFO:: total elpsd: 5.5 secs | 1.5 caribouMovement plot 10
2020-05-21 04:48:54 INFO:: total elpsd: 5.6 secs | 1.583 caribouMovement move 5
2020-05-21 04:48:54 INFO:: total elpsd: 5.6 secs | 1.583 caribouMovement plot 10
2020-05-21 04:48:54 INFO:: total elpsd: 5.8 secs | 1.667 caribouMovement move 5
2020-05-21 04:48:54 INFO:: total elpsd: 5.8 secs | 1.667 caribouMovement plot 10
2020-05-21 04:48:54 INFO:: total elpsd: 5.9 secs | 1.75 caribouMovement move 5
2020-05-21 04:48:54 INFO:: total elpsd: 5.9 secs | 1.75 caribouMovement plot 10
2020-05-21 04:48:54 INFO:: total elpsd: 6.1 secs | 1.833 caribouMovement move 5
2020-05-21 04:48:54 INFO:: total elpsd: 6.1 secs | 1.833 caribouMovement plot 10
2020-05-21 04:48:54 INFO:: total elpsd: 6.2 secs | 1.917 caribouMovement move 5
2020-05-21 04:48:54 INFO:: total elpsd: 6.2 secs | 1.917 caribouMovement plot 10
2020-05-21 04:48:54 INFO:: total elpsd: 6.3 secs | 2 fireSpread burn 5
2020-05-21 04:48:54 INFO:: total elpsd: 6.4 secs | 2 caribouMovement move 5
2020-05-21 04:48:54 INFO:: total elpsd: 6.4 secs | 2 fireSpread stats 5
2020-05-21 04:48:54 INFO:: total elpsd: 6.4 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$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Attaching package: 'raster'
The following object is masked from 'package:magrittr':
extract
Loading required package: quickPlot
Attaching package: 'SpaDES.core'
The following objects are masked from 'package:stats':
end, start
The following object is masked from 'package:utils':
citation
Setting:
options(
spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = '/private/tmp/RtmpRmsf1S/raster'
reproducible.cachePath = '/private/tmp/RtmpRmsf1S/reproducible/cache'
spades.inputPath = '/private/tmp/RtmpXjNkz0/SpaDES/inputs'
spades.outputPath = '/private/tmp/RtmpXjNkz0/SpaDES/outputs'
spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
)
--- finished re-building ‘iii-cache.Rmd’
--- re-building ‘iv-advanced.Rmd’ using rmarkdown
Warning in engine$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
Version: 1.0.1
Check: Rd cross-references
Result: WARN
Missing link or links in documentation object 'SpaDES.core-package.Rd':
'[reproducible]{cache}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
Flavor: r-oldrel-windows-ix86+x86_64
Version: 1.0.1
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 = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = 'D:/temp/RtmpaUEW44/raster'
reproducible.cachePath = 'D:/temp/RtmpaUEW44/Require/cache'
spades.inputPath = 'D:/temp/RtmpknkWtn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpknkWtn/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Loading required package: RColorBrewer
Loading required package: raster
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:quickPlot':
gpar
2020-08-05 11:53:00 INFO:: total elpsd: 0 secs | 0 checkpoint init 0
2020-08-05 11:53:00 INFO:: total elpsd: 0 secs | 0 save init 0
2020-08-05 11:53:00 INFO:: total elpsd: 0 secs | 0 progress init 0
2020-08-05 11:53:00 INFO:: total elpsd: 0.016 secs | 0 load init 0
2020-08-05 11:53:00 INFO:: total elpsd: 0.016 secs | 0 randomLandscapes init 1
2020-08-05 11:53:02 INFO:: total elpsd: 1.6 secs | 0 fireSpread init 1
2020-08-05 11:53:02 INFO:: total elpsd: 1.6 secs | 0 caribouMovement init 1
2020-08-05 11:53:02 INFO:: total elpsd: 1.6 secs | 0 fireSpread burn 5
2020-08-05 11:53:02 INFO:: total elpsd: 1.8 secs | 0 fireSpread stats 5
2020-08-05 11:53:02 INFO:: total elpsd: 1.8 secs | 0 randomLandscapes plot 10
2020-08-05 11:53:02 INFO:: total elpsd: 2.1 secs | 0 fireSpread plot.init 10
2020-08-05 11:53:02 INFO:: total elpsd: 2.3 secs | 0.08333 caribouMovement plot.init 10
2020-08-05 11:53:02 INFO:: total elpsd: 2.4 secs | 0.1667 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 2.5 secs | 0.25 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 2.6 secs | 0.3333 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 2.8 secs | 0.4167 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 2.9 secs | 0.5 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 3 secs | 0.5833 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 3.1 secs | 0.6667 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 3.2 secs | 0.75 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 3.3 secs | 0.8333 caribouMovement plot 10
2020-08-05 11:53:03 INFO:: total elpsd: 3.5 secs | 0.9167 caribouMovement plot 10
2020-08-05 11:53:04 INFO:: total elpsd: 3.6 secs | 1 caribouMovement move 5
2020-08-05 11:53:04 INFO:: total elpsd: 3.6 secs | 1 fireSpread burn 5
2020-08-05 11:53:04 INFO:: total elpsd: 4.4 secs | 1 fireSpread stats 5
2020-08-05 11:53:04 INFO:: total elpsd: 4.4 secs | 1 caribouMovement plot 10
2020-08-05 11:53:04 INFO:: total elpsd: 4.4 secs | 1.083 caribouMovement move 5
2020-08-05 11:53:04 INFO:: total elpsd: 4.5 secs | 1.083 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 4.5 secs | 1.167 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 4.5 secs | 1.167 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 4.6 secs | 1.25 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 4.6 secs | 1.25 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 4.7 secs | 1.333 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 4.7 secs | 1.333 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 4.8 secs | 1.417 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 4.8 secs | 1.417 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 4.9 secs | 1.5 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 4.9 secs | 1.5 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 4.9 secs | 1.583 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 5 secs | 1.583 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 5 secs | 1.667 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 5.1 secs | 1.667 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 5.1 secs | 1.75 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 5.1 secs | 1.75 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 5.3 secs | 1.833 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 5.3 secs | 1.833 caribouMovement plot 10
2020-08-05 11:53:05 INFO:: total elpsd: 5.4 secs | 1.917 caribouMovement move 5
2020-08-05 11:53:05 INFO:: total elpsd: 5.4 secs | 1.917 caribouMovement plot 10
2020-08-05 11:53:06 INFO:: total elpsd: 5.5 secs | 2 fireSpread burn 5
2020-08-05 11:53:06 INFO:: total elpsd: 5.6 secs | 2 caribouMovement move 5
2020-08-05 11:53:06 INFO:: total elpsd: 5.6 secs | 2 fireSpread stats 5
2020-08-05 11:53:06 INFO:: total elpsd: 5.6 secs | 2 caribouMovement plot 10
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades() call.
Setting:
options(
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = 'D:/temp/RtmpaUEW44/raster'
reproducible.cachePath = 'D:/temp/RtmpaUEW44/Require/cache'
spades.inputPath = 'D:/temp/RtmpknkWtn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpknkWtn/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = 'D:/temp/RtmpaUEW44/raster'
reproducible.cachePath = 'D:/temp/RtmpaUEW44/Require/cache'
spades.inputPath = 'D:/temp/RtmpknkWtn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpknkWtn/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = 'D:/temp/RtmpaUEW44/raster'
reproducible.cachePath = 'D:/temp/RtmpaUEW44/Require/cache'
spades.inputPath = 'D:/temp/RtmpknkWtn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpknkWtn/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Attaching package: 'data.table'
The following object is masked from 'package:raster':
shift
Setting:
options(
spades.outputPath = 'D:/temp/RtmpaUEW44/simOutputs'
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = 'D:/temp/RtmpaUEW44/raster'
reproducible.cachePath = 'D:/temp/RtmpaUEW44/Require/cache'
spades.inputPath = 'D:/temp/RtmpknkWtn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpaUEW44/simOutputs'
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
2020-08-05 11:53:08 INFO:: total elpsd: 0 secs | 0 checkpoint init 0
2020-08-05 11:53:08 INFO:: total elpsd: 0 secs | 0 save init 0
2020-08-05 11:53:08 INFO:: total elpsd: 0 secs | 0 progress init 0
2020-08-05 11:53:08 INFO:: total elpsd: 0 secs | 0 load init 0
2020-08-05 11:53:08 INFO:: total elpsd: 0.016 secs | 0 randomLandscapes init 1
2020-08-05 11:53:10 INFO:: total elpsd: 1.5 secs | 0 randomLandscapes plot 10
2020-08-05 11:53:10 INFO:: total elpsd: 1.6 secs | 0 randomLandscapes save 11
2020-08-05 11:53:10 INFO:: total elpsd: 1.6 secs | 10 save spades 10
2020-08-05 11:53:10 INFO:: total elpsd: 1.9 secs | 10 save later 10
2020-08-05 11:53:10 INFO:: total elpsd: 1.9 secs | 10 randomLandscapes save 11
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades() call.
2020-08-05 11:53:10 INFO:: total elpsd: 1.9 secs | 0 checkpoint init 0
2020-08-05 11:53:10 INFO:: total elpsd: 1.9 secs | 0 save init 0
2020-08-05 11:53:10 INFO:: total elpsd: 1.9 secs | 0 progress init 0
2020-08-05 11:53:10 INFO:: total elpsd: 1.9 secs | 0 load init 0
2020-08-05 11:53:10 INFO:: total elpsd: 1.9 secs | 0 randomLandscapes init 1
2020-08-05 11:53:11 INFO:: total elpsd: 3.1 secs | 0 randomLandscapes plot 10
2020-08-05 11:53:12 INFO:: total elpsd: 3.2 secs | 0 randomLandscapes save 11
2020-08-05 11:53:12 INFO:: total elpsd: 3.2 secs | 3 save spades 10
2020-08-05 11:53:12 INFO::Loading required namespace: logging
2020-08-05 11:53:12 INFO:: total elpsd: 3.3 secs | 3 save later 10
2020-08-05 11:53:12 INFO:: total elpsd: 3.3 secs | 6 save later 10
2020-08-05 11:53:12 INFO:: total elpsd: 3.6 secs | 6 save later 10
2020-08-05 11:53:12 INFO:: total elpsd: 3.6 secs | 10 randomLandscapes save 11
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades() call.
--- finished re-building 'ii-modules.Rmd'
--- re-building 'iii-cache.Rmd' using rmarkdown
Loading required package: sp
Attaching package: 'raster'
The following object is masked from 'package:magrittr':
extract
Loading required package: quickPlot
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 = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = 'D:/temp/RtmpQJI7w0/raster'
reproducible.cachePath = 'D:/temp/RtmpQJI7w0/Require/cache'
spades.inputPath = 'D:/temp/RtmpknkWtn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpknkWtn/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpqY1fBz/RLIBS_222a8dad23b7/SpaDES.core/sampleModules'
)
Loading required package: RColorBrewer
Loading required package: SpaDES.tools
Failed with error: 'there is no package called 'googledrive''
Quitting from lines 134-144 (iii-cache.Rmd)
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
googledrive is required but not yet installed. Try: install.packages('googledrive') to use google drive files
--- failed re-building 'iii-cache.Rmd'
--- re-building 'iv-advanced.Rmd' using rmarkdown
--- finished re-building 'iv-advanced.Rmd'
SUMMARY: processing the following file failed:
'iii-cache.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64