Last updated on 2019-10-31 00:51:08 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.6 | 50.97 | 565.06 | 616.03 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.6 | 39.94 | 456.70 | 496.64 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.6 | 668.33 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.6 | 633.21 | OK | |||
| r-devel-windows-ix86+x86_64 | 0.2.6 | 112.00 | 599.00 | 711.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.6 | 49.44 | 515.80 | 565.24 | OK | |
| r-patched-solaris-x86 | 0.2.6 | 917.30 | WARN | |||
| r-release-linux-x86_64 | 0.2.6 | 47.67 | 516.76 | 564.43 | OK | |
| r-release-windows-ix86+x86_64 | 0.2.6 | 101.00 | 412.00 | 513.00 | OK | |
| r-release-osx-x86_64 | 0.2.6 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 0.2.6 | 66.00 | 532.00 | 598.00 | OK | |
| r-oldrel-osx-x86_64 | 0.2.6 | WARN |
Version: 0.2.6
Check: tests
Result: ERROR
Running 'test-all.R' [281s/211s]
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] "<environment: 0x11dd8430>"
[1] "<environment: 0x117e0c40>"
Error in header[["Content-Length"]] : subscript out of bounds
-- 1. Error: 3 levels of parent and child modules load and show correctly (@test
object 'from' not found
1: moduleGraph(mySim, FALSE) at testthat/test-module-deps-methods.R:202
2: moduleGraph(mySim, FALSE)
3: lapply(parents, function(par) data.frame(el[from == par]))
4: FUN(X[[i]], ...)
5: data.frame(el[from == par])
6: el[from == par]
7: `[.data.frame`(el, from == par)
Vim: Warning: Output is not to a terminal
Vim: Warning: Input is not from a terminal
<1b>[m<1b>[m<1b>[0m<1b>[H<1b>[2J<1b>[24;1H</RtmpnLA9H9/AjzGsO/child_module/./child_module.R"
</AjzGsO/child_module/./child_module.R" 194L, 7282C<1b>[2;1H<1b>[34m# Everything in this file gets sourced during simInit, and all functions and obj<1b>[3;1Hects
# are put into the simList. To use objects, use sim$xxx, and are thus globally a<1b>[5;1Hvailable
# to all modules. Functions can be used without sim$ as they are namespaced, lik<1b>[7;1He functions
# in R packages. If exact location is required, functions will be: sim$<moduleNa<1b>[9;1Hme>$FunctionName<1b>[0m
<1b>[36mdefineModule<1b>[0m<1b>[35m(<1b>[0msim<1b>[35m,<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(<1b>[0m
name <1b>[33m=<1b>[0m <1b>[31m"child_module"<1b>[0m<1b>[35m,<1b>[0m
description <1b>[33m=<1b>[0m <1b>[31mNA<1b>[0m<1b>[35m,<1b>[0m <1b>[34m#"insert module description here",<1b>[0m
keywords <1b>[33m=<1b>[0m <1b>[31mNA<1b>[0m<1b>[35m,<1b>[0m <1b>[34m# c("insert key words here"),<1b>[0m
authors <1b>[33m=<1b>[0m <1b>[36mc<1b>[0m<1b>[35m(<1b>[0m<1b>[36mperson<1b>[0m<1b>[35m(<1b>[0m<1b>[36mc<1b>[0m<1b>[35m(<1b>[0m<1b>[31m"First"<1b>[0m<1b>[35m,<1b>[0m <1b>[31m"Middle"<1b>[0m<1b>[35m),<1b>[0m <1b>[31m"Last"<1b>[0m<1b>[35m,<1b>[0m email <1b>[33m=<1b>[0m <1b>[31m"email@example.com"<1b>[0m<1b>[35m,<1b>[0m
role <1b>[33m=<1b>[0m <1b>[36mc<1b>[0m<1b>[35m(<1b>[0m<1b>[31m"aut"<1b>[0m<1b>[35m,<1b>[0m <1b>[31m"cre"<1b>[0m<1b>[35m))),<1b>[0m
childModules <1b>[33m=<1b>[0m <1b>[32mcharacter<1b>[0m<1b>[35m(<1b>[0m<1b>[31m0<1b>[0m<1b>[35m),<1b>[0m
version <1b>[33m=<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(<1b>[0mSpaDES.core <1b>[33m=<1b>[0m <1b>[31m"0.2.6"<1b>[0m<1b>[35m,<1b>[0m child_module <1b>[33m=<1b>[0m <1b>[31m"0.0.1"<1b>[0m<1b>[35m),<1b>[0m
spatialExtent <1b>[33m=<1b>[0m raster<1b>[35m::<1b>[0m<1b>[36mextent<1b>[0m<1b>[35m(<1b>[0m<1b>[36mrep<1b>[0m<1b>[35m(<1b>[0m<1b>[31mNA_real_<1b>[0m<1b>[35m,<1b>[0m <1b>[31m4<1b>[0m<1b>[35m)),<1b>[0m
timeframe <1b>[33m=<1b>[0m <1b>[36mas.POSIXlt<1b>[0m<1b>[35m(<1b>[0m<1b>[36mc<1b>[0m<1b>[35m(<1b>[0m<1b>[31mNA<1b>[0m<1b>[35m,<1b>[0m <1b>[31mNA<1b>[0m<1b>[35m)),<1b>[0m
timeunit <1b>[33m=<1b>[0m <1b>[31m"year"<1b>[0m<1b>[35m,<1b>[0m
citation <1b>[33m=<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(<1b>[0m<1b>[31m"citation.bib"<1b>[0m<1b>[35m),<1b>[0m
documentation <1b>[33m=<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(<1b>[0m<1b>[31m"README.txt"<1b>[0m<1b>[35m,<1b>[0m <1b>[31m"child_module.Rmd"<1b>[0m<1b>[35m),<1b>[0m
reqdPkgs <1b>[33m=<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(),<1b>[0m<1b>[24;63H1,0-1<1b>[9CTop<1b>[1;1H<1b>[24;1HVim: Error reading input, exiting...
Vim: Finished.
<1b>[24;1H
Vim: Warning: Output is not to a terminal
Vim: Warning: Input is not from a terminal
<1b>[m<1b>[m<1b>[0m<1b>[H<1b>[2J<1b>[24;1H<tmpnLA9H9/AjzGsO/child_module/./child_module.Rmd"
<AjzGsO/child_module/./child_module.Rmd" 74L, 1677C<1b>[1;1H<1b>[35m---<1b>[0m
<1b>[36mtitle<1b>[0m: "<1b>[31mchild_module<1b>[0m"
<1b>[36mauthor<1b>[0m: ""
<1b>[36mdate<1b>[0m: "<1b>[31m29 October 2019<1b>[0m"
<1b>[36moutput<1b>[0m: pdf_document
<1b>[35m---
#<1b>[0m<1b>[35m Overview<1b>[0m
Provide an overview of what the module does / how to use the module.
Module documentation should be written so that others can use your module.
This is a template for module documentation, and should be changed to reflect yo<1b>[14;1Hur module.
<1b>[35m##<1b>[0m<1b>[35m R Markdown<1b>[0m
R Markdown syntax allows R code, outputs, and figures to be rendered in the docu<1b>[19;1Hmentation.
For help writing in R Markdown, see http://rmarkdown.rstudio.com/.
<1b>[35m#<1b>[0m<1b>[35m Usage<1b>[0m<1b>[24;63H1,1<1b>[11CTop<1b>[1;1H<1b>[24;1HVim: Error reading input, exiting...
Vim: Finished.
<1b>[24;1H
Vim: Warning: Output is not to a terminal
Vim: Warning: Input is not from a terminal
<1b>[m<1b>[m<1b>[0m<1b>[H<1b>[2J<1b>[24;1H<tmpnLA9H9/AjzGsO/parent_module/./parent_module.R"
</AjzGsO/parent_module/./parent_module.R" 18L, 902C<1b>[2;1H<1b>[34m# Everything in this file gets sourced during simInit, and all functions and obj<1b>[3;1Hects
# are put into the simList. To use objects, use sim$xxx, and are thus globally a<1b>[5;1Hvailable
# to all modules. Functions can be used without sim$ as they are namespaced, lik<1b>[7;1He functions
# in R packages. If exact location is required, functions will be: sim$<moduleNa<1b>[9;1Hme>$FunctionName<1b>[0m
<1b>[36mdefineModule<1b>[0m<1b>[35m(<1b>[0msim<1b>[35m,<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(<1b>[0m
name <1b>[33m=<1b>[0m <1b>[31m"parent_module"<1b>[0m<1b>[35m,<1b>[0m
description <1b>[33m=<1b>[0m <1b>[31mNA<1b>[0m<1b>[35m,<1b>[0m <1b>[34m#"insert module description here",<1b>[0m
keywords <1b>[33m=<1b>[0m <1b>[31mNA<1b>[0m<1b>[35m,<1b>[0m <1b>[34m# c("insert key words here"),<1b>[0m
authors <1b>[33m=<1b>[0m <1b>[36mc<1b>[0m<1b>[35m(<1b>[0m<1b>[36mperson<1b>[0m<1b>[35m(<1b>[0m<1b>[36mc<1b>[0m<1b>[35m(<1b>[0m<1b>[31m"First"<1b>[0m<1b>[35m,<1b>[0m <1b>[31m"Middle"<1b>[0m<1b>[35m),<1b>[0m <1b>[31m"Last"<1b>[0m<1b>[35m,<1b>[0m email <1b>[33m=<1b>[0m <1b>[31m"email@example.com"<1b>[0m<1b>[35m,<1b>[0m
role <1b>[33m=<1b>[0m <1b>[36mc<1b>[0m<1b>[35m(<1b>[0m<1b>[31m"aut"<1b>[0m<1b>[35m,<1b>[0m <1b>[31m"cre"<1b>[0m<1b>[35m))),<1b>[0m
childModules <1b>[33m=<1b>[0m <1b>[31m"child_module"<1b>[0m<1b>[35m,<1b>[0m
version <1b>[33m=<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(<1b>[0mSpaDES.core <1b>[33m=<1b>[0m <1b>[31m"0.2.6"<1b>[0m<1b>[35m,<1b>[0m parent_module <1b>[33m=<1b>[0m <1b>[31m"0.0.1"<1b>[0m<1b>[35m,<1b>[0m child_module <1b>[33m=<1b>[0m
<1b>[31m"0.0.1"<1b>[0m<1b>[35m),<1b>[0m
timeframe <1b>[33m=<1b>[0m <1b>[36mas.POSIXlt<1b>[0m<1b>[35m(<1b>[0m<1b>[36mc<1b>[0m<1b>[35m(<1b>[0m<1b>[31mNA<1b>[0m<1b>[35m,<1b>[0m <1b>[31mNA<1b>[0m<1b>[35m)),<1b>[0m
timeunit <1b>[33m=<1b>[0m <1b>[31m"year"<1b>[0m<1b>[35m,<1b>[0m
citation <1b>[33m=<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(<1b>[0m<1b>[31m"citation.bib"<1b>[0m<1b>[35m),<1b>[0m
documentation <1b>[33m=<1b>[0m <1b>[32mlist<1b>[0m<1b>[35m(<1b>[0m<1b>[31m"README.txt"<1b>[0m<1b>[35m,<1b>[0m <1b>[31m"parent_module.Rmd"<1b>[0m<1b>[35m)<1b>[0m<1b>[24;63H1,0-1<1b>[9CTop<1b>[1;1H<1b>[24;1HVim: Error reading input, exiting...
Vim: Finished.
<1b>[24;1H
Vim: Warning: Output is not to a terminal
Vim: Warning: Input is not from a terminal
<1b>[m<1b>[m<1b>[0m<1b>[H<1b>[2J<1b>[24;1H<pnLA9H9/AjzGsO/parent_module/./parent_module.Rmd"
<zGsO/parent_module/./parent_module.Rmd" 74L, 1680C<1b>[1;1H<1b>[35m---<1b>[0m
<1b>[36mtitle<1b>[0m: "<1b>[31mparent_module<1b>[0m"
<1b>[36mauthor<1b>[0m: ""
<1b>[36mdate<1b>[0m: "<1b>[31m29 October 2019<1b>[0m"
<1b>[36moutput<1b>[0m: pdf_document
<1b>[35m---
#<1b>[0m<1b>[35m Overview<1b>[0m
Provide an overview of what the module does / how to use the module.
Module documentation should be written so that others can use your module.
This is a template for module documentation, and should be changed to reflect yo<1b>[14;1Hur module.
<1b>[35m##<1b>[0m<1b>[35m R Markdown<1b>[0m
R Markdown syntax allows R code, outputs, and figures to be rendered in the docu<1b>[19;1Hmentation.
For help writing in R Markdown, see http://rmarkdown.rstudio.com/.
<1b>[35m#<1b>[0m<1b>[35m Usage<1b>[0m<1b>[24;63H1,1<1b>[11CTop<1b>[1;1H<1b>[24;1HVim: Error reading input, exiting...
Vim: Finished.
<1b>[24;1H
== testthat results ===========================================================
[ OK: 480 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 1 ]
1. Error: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#202)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.6
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 = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpXI1Cx3/reproducible/cache'
spades.inputPath = '/tmp/RtmpukcpUP/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpukcpUP/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpXI1Cx3/reproducible/cache'
spades.inputPath = '/tmp/RtmpukcpUP/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpukcpUP/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/SpaDES.core/sampleModules'
)
Quitting from lines 474-495 (ii-modules.Rmd)
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
object 'from' not found
--- failed 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
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
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpdpaLCB/reproducible/cache'
spades.inputPath = '/tmp/RtmpukcpUP/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpukcpUP/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/SpaDES.core/sampleModules'
)
--- finished re-building 'iii-cache.Rmd'
SUMMARY: processing the following file failed:
'ii-modules.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.6
Check: tests
Result: ERROR
Running 'test-all.R' [203s]
Flavor: r-devel-windows-ix86+x86_64
Version: 0.2.6
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:/RCompile/CRANpkg/lib/3.7/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpSSffjL/reproducible/cache'
spades.inputPath = 'D:/temp/Rtmp8OUR2Y/SpaDES/inputs'
spades.outputPath = 'D:/temp/Rtmp8OUR2Y/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/3.7/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Setting:
options(
spades.modulePath = 'D:/RCompile/CRANpkg/lib/3.7/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpSSffjL/reproducible/cache'
spades.inputPath = 'D:/temp/Rtmp8OUR2Y/SpaDES/inputs'
spades.outputPath = 'D:/temp/Rtmp8OUR2Y/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/3.7/SpaDES.core/sampleModules'
)
Quitting from lines 474-495 (ii-modules.Rmd)
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
object 'from' not found
--- failed 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
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
Setting:
options(
spades.modulePath = 'D:/RCompile/CRANpkg/lib/3.7/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpWc0Reo/reproducible/cache'
spades.inputPath = 'D:/temp/Rtmp8OUR2Y/SpaDES/inputs'
spades.outputPath = 'D:/temp/Rtmp8OUR2Y/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/3.7/SpaDES.core/sampleModules'
)
--- finished re-building 'iii-cache.Rmd'
SUMMARY: processing the following file failed:
'ii-modules.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 0.2.6
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(
reproducible.cachePath = '/tmp/RtmpEzayYq/reproducible/cache'
spades.inputPath = '/tmp/Rtmpzeaqdw/SpaDES/inputs'
spades.outputPath = '/tmp/Rtmpzeaqdw/SpaDES/outputs'
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Quitting from lines 376-380 (ii-modules.Rmd)
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ii-modules.Rmd’
--- re-building ‘iii-cache.Rmd’ using rmarkdown
Warning in engine$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
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
Setting:
options(
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpmJaOzD/reproducible/cache'
spades.inputPath = '/tmp/Rtmpzeaqdw/SpaDES/inputs'
spades.outputPath = '/tmp/Rtmpzeaqdw/SpaDES/outputs'
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
--- finished re-building ‘iii-cache.Rmd’
SUMMARY: processing the following file failed:
‘ii-modules.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.2.6
Check: dependencies in R code
Result: NOTE
No protocol specified
No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.6
Check: S3 generic/method consistency
Result: WARN
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.6
Check: replacement functions
Result: WARN
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.6
Check: foreign function calls
Result: NOTE
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.6
Check: R code for possible problems
Result: NOTE
No protocol specified
No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.6
Check: for missing documentation entries
Result: WARN
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.6
Check: for code/documentation mismatches
Result: WARN
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.6
Check: Rd \usage sections
Result: NOTE
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64
Version: 0.2.6
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
No protocol specified
No protocol specified
Warning in fun(libname, pkgname) : couldn't connect to display ":0"
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(
reproducible.cachePath = '/private/tmp/RtmpIWU0pA/reproducible/cache'
spades.inputPath = '/private/tmp/RtmpmXyOGl/SpaDES/inputs'
spades.outputPath = '/private/tmp/RtmpmXyOGl/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'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Quitting from lines 376-380 (ii-modules.Rmd)
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ii-modules.Rmd’
--- re-building ‘iii-cache.Rmd’ using rmarkdown
Warning in engine$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
Loading required package: reproducible
No protocol specified
No protocol specified
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(
reproducible.cachePath = '/private/tmp/RtmpSRuC5R/reproducible/cache'
spades.inputPath = '/private/tmp/RtmpmXyOGl/SpaDES/inputs'
spades.outputPath = '/private/tmp/RtmpmXyOGl/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’
SUMMARY: processing the following file failed:
‘ii-modules.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-osx-x86_64
Version: 0.2.6
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
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/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/private/tmp/RtmpueqZJa/reproducible/cache'
spades.inputPath = '/private/tmp/RtmpWP0dYl/SpaDES/inputs'
spades.outputPath = '/private/tmp/RtmpWP0dYl/SpaDES/outputs'
spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Quitting from lines 376-380 (ii-modules.Rmd)
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Flavor: r-oldrel-osx-x86_64