Last updated on 2020-07-16 15:49:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 45.13 | 674.74 | 719.87 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 38.44 | 558.86 | 597.30 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 722.80 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 793.37 | OK | |||
| r-devel-windows-ix86+x86_64 | 1.0.1 | 127.00 | 668.00 | 795.00 | OK | |
| r-patched-linux-x86_64 | 1.0.1 | 44.44 | 637.69 | 682.13 | OK | |
| r-patched-solaris-x86 | 1.0.1 | 940.00 | WARN | |||
| r-release-linux-x86_64 | 1.0.1 | 46.99 | 626.71 | 673.70 | OK | |
| r-release-windows-ix86+x86_64 | 1.0.1 | 115.00 | 695.00 | 810.00 | OK | |
| r-oldrel-macos-x86_64 | 1.0.1 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.1 | 107.00 | 674.00 | 781.00 | OK |
Version: 1.0.1
Check: Rd cross-references
Result: NOTE
Undeclared package ‘sp’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
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 = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = '/tmp/RtmpP3aW22/working_dir/RtmpYCaiwt/raster'
reproducible.cachePath = '/tmp/RtmpP3aW22/working_dir/RtmpYCaiwt/reproducible/cache'
spades.inputPath = '/tmp/RtmpNVaWXX/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpNVaWXX/SpaDES/outputs'
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
2020-07-16 06:49:56 INFO:: total elpsd: 0.0072 secs | 0 checkpoint init 0
2020-07-16 06:49:56 INFO:: total elpsd: 0.018 secs | 0 save init 0
2020-07-16 06:49:56 INFO:: total elpsd: 0.024 secs | 0 progress init 0
2020-07-16 06:49:56 INFO:: total elpsd: 0.029 secs | 0 load init 0
2020-07-16 06:49:56 INFO:: total elpsd: 0.034 secs | 0 randomLandscapes init 1
2020-07-16 06:50:00 INFO:: total elpsd: 3.8 secs | 0 fireSpread init 1
2020-07-16 06:50:00 INFO:: total elpsd: 3.8 secs | 0 caribouMovement init 1
2020-07-16 06:50:00 INFO:: total elpsd: 3.9 secs | 0 fireSpread burn 5
2020-07-16 06:50:00 INFO:: total elpsd: 4.1 secs | 0 fireSpread stats 5
2020-07-16 06:50:00 INFO:: total elpsd: 4.1 secs | 0 randomLandscapes plot 10
2020-07-16 06:50:01 INFO:: total elpsd: 4.4 secs | 0 fireSpread plot.init 10
2020-07-16 06:50:01 INFO:: total elpsd: 4.7 secs | 0.08333 caribouMovement plot.init 10
2020-07-16 06:50:01 INFO:: total elpsd: 4.8 secs | 0.1667 caribouMovement plot 10
2020-07-16 06:50:01 INFO:: total elpsd: 5 secs | 0.25 caribouMovement plot 10
2020-07-16 06:50:01 INFO:: total elpsd: 5.2 secs | 0.3333 caribouMovement plot 10
2020-07-16 06:50:02 INFO:: total elpsd: 5.3 secs | 0.4167 caribouMovement plot 10
2020-07-16 06:50:02 INFO:: total elpsd: 5.5 secs | 0.5 caribouMovement plot 10
2020-07-16 06:50:02 INFO:: total elpsd: 5.6 secs | 0.5833 caribouMovement plot 10
2020-07-16 06:50:02 INFO:: total elpsd: 5.8 secs | 0.6667 caribouMovement plot 10
2020-07-16 06:50:02 INFO:: total elpsd: 5.9 secs | 0.75 caribouMovement plot 10
2020-07-16 06:50:02 INFO:: total elpsd: 6.1 secs | 0.8333 caribouMovement plot 10
2020-07-16 06:50:02 INFO:: total elpsd: 6.3 secs | 0.9167 caribouMovement plot 10
2020-07-16 06:50:03 INFO:: total elpsd: 6.4 secs | 1 caribouMovement move 5
2020-07-16 06:50:03 INFO:: total elpsd: 6.5 secs | 1 fireSpread burn 5
2020-07-16 06:50:04 INFO:: total elpsd: 7.9 secs | 1 fireSpread stats 5
2020-07-16 06:50:04 INFO:: total elpsd: 7.9 secs | 1 caribouMovement plot 10
2020-07-16 06:50:04 INFO:: total elpsd: 8.1 secs | 1.083 caribouMovement move 5
2020-07-16 06:50:04 INFO:: total elpsd: 8.1 secs | 1.083 caribouMovement plot 10
2020-07-16 06:50:05 INFO:: total elpsd: 8.3 secs | 1.167 caribouMovement move 5
2020-07-16 06:50:05 INFO:: total elpsd: 8.3 secs | 1.167 caribouMovement plot 10
2020-07-16 06:50:05 INFO:: total elpsd: 8.5 secs | 1.25 caribouMovement move 5
2020-07-16 06:50:05 INFO:: total elpsd: 8.5 secs | 1.25 caribouMovement plot 10
2020-07-16 06:50:05 INFO:: total elpsd: 8.6 secs | 1.333 caribouMovement move 5
2020-07-16 06:50:05 INFO:: total elpsd: 8.7 secs | 1.333 caribouMovement plot 10
2020-07-16 06:50:05 INFO:: total elpsd: 8.8 secs | 1.417 caribouMovement move 5
2020-07-16 06:50:05 INFO:: total elpsd: 8.8 secs | 1.417 caribouMovement plot 10
2020-07-16 06:50:05 INFO:: total elpsd: 9 secs | 1.5 caribouMovement move 5
2020-07-16 06:50:05 INFO:: total elpsd: 9 secs | 1.5 caribouMovement plot 10
2020-07-16 06:50:05 INFO:: total elpsd: 9.2 secs | 1.583 caribouMovement move 5
2020-07-16 06:50:05 INFO:: total elpsd: 9.2 secs | 1.583 caribouMovement plot 10
2020-07-16 06:50:06 INFO:: total elpsd: 9.4 secs | 1.667 caribouMovement move 5
2020-07-16 06:50:06 INFO:: total elpsd: 9.4 secs | 1.667 caribouMovement plot 10
2020-07-16 06:50:06 INFO:: total elpsd: 9.6 secs | 1.75 caribouMovement move 5
2020-07-16 06:50:06 INFO:: total elpsd: 9.6 secs | 1.75 caribouMovement plot 10
2020-07-16 06:50:06 INFO:: total elpsd: 9.7 secs | 1.833 caribouMovement move 5
2020-07-16 06:50:06 INFO:: total elpsd: 9.8 secs | 1.833 caribouMovement plot 10
2020-07-16 06:50:06 INFO:: total elpsd: 9.9 secs | 1.917 caribouMovement move 5
2020-07-16 06:50:06 INFO:: total elpsd: 9.9 secs | 1.917 caribouMovement plot 10
2020-07-16 06:50:06 INFO:: total elpsd: 10 secs | 2 fireSpread burn 5
2020-07-16 06:50:06 INFO:: total elpsd: 10 secs | 2 caribouMovement move 5
2020-07-16 06:50:06 INFO:: total elpsd: 10 secs | 2 fireSpread stats 5
2020-07-16 06:50:06 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/RtmpP3aW22/working_dir/RtmpIkaWNt/raster'
reproducible.cachePath = '/tmp/RtmpP3aW22/working_dir/RtmpIkaWNt/reproducible/cache'
spades.inputPath = '/tmp/RtmpNVaWXX/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpNVaWXX/SpaDES/outputs'
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
--- finished re-building ‘iii-cache.Rmd’
--- re-building ‘iv-advanced.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘iv-advanced.Rmd’
SUMMARY: processing the following file failed:
‘ii-modules.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.0.1
Check: dependencies in R code
Result: NOTE
No protocol specified
No protocol specified
Flavor: r-oldrel-macos-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘i-introduction.Rmd’ using rmarkdown
Warning in engine$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