Last updated on 2019-11-26 00:52:13 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.6 | 55.53 | 574.40 | 629.93 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.6 | 43.15 | 473.53 | 516.68 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.7 | 641.62 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.7 | 616.98 | OK | |||
| r-devel-windows-ix86+x86_64 | 0.2.6 | 118.00 | 575.00 | 693.00 | ERROR | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.2.6 | 78.00 | 453.00 | 531.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.6 | 52.76 | 525.37 | 578.13 | ERROR | |
| r-patched-solaris-x86 | 0.2.7 | 670.40 | WARN | |||
| r-release-linux-x86_64 | 0.2.6 | 49.87 | 537.50 | 587.37 | ERROR | |
| r-release-windows-ix86+x86_64 | 0.2.7 | 73.00 | 407.00 | 480.00 | OK | |
| r-release-osx-x86_64 | 0.2.6 | WARN | ||||
| r-oldrel-windows-ix86+x86_64 | 0.2.6 | 41.00 | 387.00 | 428.00 | ERROR | |
| r-oldrel-osx-x86_64 | 0.2.6 | WARN |
Version: 0.2.6
Check: tests
Result: ERROR
Running 'test-all.R' [276s/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. Error: test cache (@test-cache.R#34) ------------------------------------
is.character(repoDir) & length(repoDir) == 1 is not TRUE
Backtrace:
1. reproducible::showCache(sims[[1]])
2. reproducible::showCache(sims[[1]])
6. archivist::showLocalRepo(x)
7. base::stopifnot(is.character(repoDir) & length(repoDir) == 1)
[1] "<environment: 0x13eeb3d8>"
[1] "<environment: 0x9d040a8>"
Error in header[["Content-Length"]] : subscript out of bounds
-- 2. Error: 3 levels of parent and child modules load and show correctly (@test
object 'from' not found
Backtrace:
1. SpaDES.core::moduleGraph(mySim, FALSE)
2. SpaDES.core::moduleGraph(mySim, FALSE)
3. base::lapply(parents, function(par) data.frame(el[from == par]))
4. SpaDES.core:::FUN(X[[i]], ...)
7. base::`[.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</RtmpIldoqE/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<tmpIldoqE/AjzGsO/child_module/./child_module.Rmd"
<AjzGsO/child_module/./child_module.Rmd" 74L, 1678C<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>[31m24 November 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<tmpIldoqE/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<pIldoqE/AjzGsO/parent_module/./parent_module.Rmd"
<zGsO/parent_module/./parent_module.Rmd" 74L, 1681C<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>[31m24 November 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: 470 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 2 ]
1. Error: test cache (@test-cache.R#34)
2. 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/Rtmp0KjfhV/reproducible/cache'
spades.inputPath = '/tmp/RtmpsaSGRn/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpsaSGRn/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/Rtmp0KjfhV/reproducible/cache'
spades.inputPath = '/tmp/RtmpsaSGRn/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpsaSGRn/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/RtmpT1J5hu/reproducible/cache'
spades.inputPath = '/tmp/RtmpsaSGRn/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpsaSGRn/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/SpaDES.core/sampleModules'
)
Quitting from lines 205-215 (iii-cache.Rmd)
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
is.character(repoDir) & length(repoDir) == 1 is not TRUE
--- failed re-building 'iii-cache.Rmd'
SUMMARY: processing the following files failed:
'ii-modules.Rmd' 'iii-cache.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’ [231s/317s]
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. Error: test cache (@test-cache.R#34) ────────────────────────────────────
is.character(repoDir) & length(repoDir) == 1 is not TRUE
Backtrace:
1. reproducible::showCache(sims[[1]])
2. reproducible::showCache(sims[[1]])
6. archivist::showLocalRepo(x)
7. base::stopifnot(is.character(repoDir) & length(repoDir) == 1)
[1] "<environment: 0x557b464925a0>"
[1] "<environment: 0x557b3c2b7db0>"
Error in header[["Content-Length"]] : subscript out of bounds
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"~/tmp/scratch/RtmpdtWY62/AjzGsO/child_module/./child_module.R" 194 lines, 7282
characters
<1b>[32mPress ENTER or type command to continue
<1b>[0mVim: 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"~/tmp/scratch/RtmpdtWY62/AjzGsO/child_module/./child_module.Rmd" 74 lines, 169
<1b>[23;80H8<1b>[24;2Hcharacters
<1b>[32mPress ENTER or type command to continue
<1b>[0mVim: 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"~/tmp/scratch/RtmpdtWY62/AjzGsO/parent_module/./parent_module.R" 18 lines, 902
characters
<1b>[32mPress ENTER or type command to continue
<1b>[0mVim: 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"~/tmp/scratch/RtmpdtWY62/AjzGsO/parent_module/./parent_module.Rmd" 74 lines, 1
<1b>[23;80H7<1b>[24;1H01 characters
<1b>[32mPress ENTER or type command to continue
<1b>[0mVim: Error reading input, exiting...
Vim: Finished.
<1b>[24;1H
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 470 | SKIPPED: 10 | WARNINGS: 0 | FAILED: 1 ]
1. Error: test cache (@test-cache.R#34)
Error: testthat unit tests failed
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
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-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/home/hornik/tmp/scratch/RtmpsiTLq9/reproducible/cache'
spades.inputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/inputs'
spades.outputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/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-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/home/hornik/tmp/scratch/RtmpsiTLq9/reproducible/cache'
spades.inputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/inputs'
spades.outputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
GLPK not found on this system.
igraph is used internally and requires a GLPK installation.
It can be installed using, e.g., `apt install libglpk-dev`.
If GLPK is installed you should reinstall igraph from source using:
`install.packages('igraph', type = 'source')`
For more info see https://github.com/igraph/rigraph/issues/273.
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/home/hornik/tmp/scratch/RtmpsiTLq9/reproducible/cache'
spades.inputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/inputs'
spades.outputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/home/hornik/tmp/scratch/RtmpsiTLq9/reproducible/cache'
spades.inputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/inputs'
spades.outputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Attaching package: 'data.table'
The following object is masked from 'package:raster':
shift
Setting:
options(
spades.outputPath = '/home/hornik/tmp/scratch/RtmpsiTLq9/simOutputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/home/hornik/tmp/scratch/RtmpsiTLq9/reproducible/cache'
spades.inputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/inputs'
spades.outputPath = '/home/hornik/tmp/scratch/RtmpsiTLq9/simOutputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
simList saved in
SpaDES.core:::.pkgEnv$.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
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-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/home/hornik/tmp/scratch/Rtmp1qxIXn/reproducible/cache'
spades.inputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/inputs'
spades.outputPath = '/home/hornik/tmp/scratch/RtmphOcl5Z/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Quitting from lines 205-215 (iii-cache.Rmd)
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
is.character(repoDir) & length(repoDir) == 1 is not TRUE
--- failed re-building ‘iii-cache.Rmd’
SUMMARY: processing the following file failed:
‘iii-cache.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.6
Check: tests
Result: ERROR
Running 'test-all.R' [193s]
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/4.0/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpMRzJw8/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpOynEpn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpOynEpn/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/4.0/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/4.0/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpMRzJw8/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpOynEpn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpOynEpn/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/4.0/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/4.0/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpKc9K16/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpOynEpn/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpOynEpn/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/4.0/SpaDES.core/sampleModules'
)
Quitting from lines 205-215 (iii-cache.Rmd)
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
is.character(repoDir) & length(repoDir) == 1 is not TRUE
--- failed re-building 'iii-cache.Rmd'
SUMMARY: processing the following files failed:
'ii-modules.Rmd' 'iii-cache.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 0.2.6
Check: tests
Result: ERROR
Running 'test-all.R' [183s]
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. Error: test cache (@test-cache.R#34) ------------------------------------
is.character(repoDir) & length(repoDir) == 1 is not TRUE
Backtrace:
1. reproducible::showCache(sims[[1]])
2. reproducible::showCache(sims[[1]])
6. archivist::showLocalRepo(x)
7. base::stopifnot(is.character(repoDir) & length(repoDir) == 1)
[1] "<environment: 0x0000000029a26c08>"
[1] "<environment: 0x000000001f2e6c30>"
-- 2. Error: 3 levels of parent and child modules load and show correctly (@test
object 'from' not found
Backtrace:
1. SpaDES.core::moduleGraph(mySim, FALSE)
2. SpaDES.core::moduleGraph(mySim, FALSE)
3. base::lapply(parents, function(par) data.frame(el[from == par]))
4. SpaDES.core:::FUN(X[[i]], ...)
7. base::`[.data.frame`(el, from == par)
== testthat results ===========================================================
[ OK: 469 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 2 ]
1. Error: test cache (@test-cache.R#34)
2. 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-windows-ix86+x86_64-gcc8
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/4.0gcc8/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpY16wK5/reproducible/cache'
spades.inputPath = 'D:/temp/Rtmpo9aHXY/SpaDES/inputs'
spades.outputPath = 'D:/temp/Rtmpo9aHXY/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/4.0gcc8/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/4.0gcc8/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpY16wK5/reproducible/cache'
spades.inputPath = 'D:/temp/Rtmpo9aHXY/SpaDES/inputs'
spades.outputPath = 'D:/temp/Rtmpo9aHXY/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/4.0gcc8/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/4.0gcc8/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/Rtmp821eKm/reproducible/cache'
spades.inputPath = 'D:/temp/Rtmpo9aHXY/SpaDES/inputs'
spades.outputPath = 'D:/temp/Rtmpo9aHXY/SpaDES/outputs'
spades.modulePath = 'D:/RCompile/CRANpkg/lib/4.0gcc8/SpaDES.core/sampleModules'
)
Quitting from lines 205-215 (iii-cache.Rmd)
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
is.character(repoDir) & length(repoDir) == 1 is not TRUE
--- failed re-building 'iii-cache.Rmd'
SUMMARY: processing the following files failed:
'ii-modules.Rmd' 'iii-cache.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8
Version: 0.2.6
Check: tests
Result: ERROR
Running ‘test-all.R’ [238s/263s]
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. Error: test cache (@test-cache.R#34) ────────────────────────────────────
is.character(repoDir) & length(repoDir) == 1 is not TRUE
Backtrace:
1. reproducible::showCache(sims[[1]])
2. reproducible::showCache(sims[[1]])
6. archivist::showLocalRepo(x)
7. base::stopifnot(is.character(repoDir) & length(repoDir) == 1)
[1] "<environment: 0x55dcd5d54b78>"
[1] "<environment: 0x55dcd9d8af48>"
Error in header[["Content-Length"]] : subscript out of bounds
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</Rtmp6Nc3NS/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<tmp6Nc3NS/AjzGsO/child_module/./child_module.Rmd"
<AjzGsO/child_module/./child_module.Rmd" 74L, 1678C<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>[31m25 November 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<tmp6Nc3NS/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<p6Nc3NS/AjzGsO/parent_module/./parent_module.Rmd"
<zGsO/parent_module/./parent_module.Rmd" 74L, 1681C<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>[31m25 November 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: 476 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 1 ]
1. Error: test cache (@test-cache.R#34)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-linux-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 = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpQnKPlk/reproducible/cache'
spades.inputPath = '/tmp/RtmpUPh3lu/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpUPh3lu/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpQnKPlk/reproducible/cache'
spades.inputPath = '/tmp/RtmpUPh3lu/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpUPh3lu/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpQnKPlk/reproducible/cache'
spades.inputPath = '/tmp/RtmpUPh3lu/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpUPh3lu/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpQnKPlk/reproducible/cache'
spades.inputPath = '/tmp/RtmpUPh3lu/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpUPh3lu/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Attaching package: 'data.table'
The following object is masked from 'package:raster':
shift
Setting:
options(
spades.outputPath = '/tmp/RtmpQnKPlk/simOutputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpQnKPlk/reproducible/cache'
spades.inputPath = '/tmp/RtmpUPh3lu/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpQnKPlk/simOutputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
--- finished re-building ‘ii-modules.Rmd’
--- re-building ‘iii-cache.Rmd’ using rmarkdown
Loading required package: sp
Attaching package: 'raster'
The following object is masked from 'package:magrittr':
extract
Loading required package: quickPlot
Loading required package: reproducible
Attaching package: 'SpaDES.core'
The following objects are masked from 'package:stats':
end, start
The following object is masked from 'package:utils':
citation
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/Rtmpp3fSKE/reproducible/cache'
spades.inputPath = '/tmp/RtmpUPh3lu/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpUPh3lu/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Quitting from lines 205-215 (iii-cache.Rmd)
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
is.character(repoDir) & length(repoDir) == 1 is not TRUE
--- failed re-building ‘iii-cache.Rmd’
SUMMARY: processing the following file failed:
‘iii-cache.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.2.7
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘i-introduction.Rmd’ using rmarkdown
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: quickPlot
Loading required package: reproducible
Attaching package: 'SpaDES.core'
The following objects are masked from 'package:stats':
end, start
The following object is masked from 'package:utils':
citation
Loading required package: SpaDES.tools
Loading required package: RandomFields
Loading required package: sp
Loading required package: RandomFieldsUtils
Attaching package: 'RandomFields'
The following object is masked from 'package:RandomFieldsUtils':
RFoptions
Setting:
options(
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = '/tmp/Rtmp4faqBx/working_dir/Rtmpa4ayqx/raster'
reproducible.cachePath = '/tmp/Rtmp4faqBx/working_dir/Rtmpa4ayqx/reproducible/cache'
spades.inputPath = '/tmp/RtmpsoaiiT/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpsoaiiT/SpaDES/outputs'
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.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$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Attaching package: 'raster'
The following object is masked from 'package:magrittr':
extract
Loading required package: quickPlot
Attaching package: 'SpaDES.core'
The following objects are masked from 'package:stats':
end, start
The following object is masked from 'package:utils':
citation
Setting:
options(
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
Paths set to:
options(
rasterTmpDir = '/tmp/Rtmp4faqBx/working_dir/RtmpK6aOBx/raster'
reproducible.cachePath = '/tmp/Rtmp4faqBx/working_dir/RtmpK6aOBx/reproducible/cache'
spades.inputPath = '/tmp/RtmpsoaiiT/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpsoaiiT/SpaDES/outputs'
spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
)
--- finished re-building ‘iii-cache.Rmd’
--- re-building ‘iv-advanced.Rmd’ using rmarkdown
Warning in engine$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: 0.2.6
Check: tests
Result: ERROR
Running ‘test-all.R’ [244s/274s]
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. Error: test cache (@test-cache.R#34) ────────────────────────────────────
is.character(repoDir) & length(repoDir) == 1 is not TRUE
Backtrace:
1. reproducible::showCache(sims[[1]])
2. reproducible::showCache(sims[[1]])
6. archivist::showLocalRepo(x)
7. base::stopifnot(is.character(repoDir) & length(repoDir) == 1)
[1] "<environment: 0x5614c80cc0c8>"
[1] "<environment: 0x5614cc5d99b8>"
Error in header[["Content-Length"]] : subscript out of bounds
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</Rtmp8hLY20/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<tmp8hLY20/AjzGsO/child_module/./child_module.Rmd"
<AjzGsO/child_module/./child_module.Rmd" 74L, 1678C<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>[31m23 November 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<tmp8hLY20/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<p8hLY20/AjzGsO/parent_module/./parent_module.Rmd"
<zGsO/parent_module/./parent_module.Rmd" 74L, 1681C<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>[31m23 November 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: 476 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 1 ]
1. Error: test cache (@test-cache.R#34)
Error: testthat unit tests failed
Execution halted
Flavor: r-release-linux-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 = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpMhWvQg/reproducible/cache'
spades.inputPath = '/tmp/RtmpCK1hIL/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpCK1hIL/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpMhWvQg/reproducible/cache'
spades.inputPath = '/tmp/RtmpCK1hIL/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpCK1hIL/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpMhWvQg/reproducible/cache'
spades.inputPath = '/tmp/RtmpCK1hIL/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpCK1hIL/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpMhWvQg/reproducible/cache'
spades.inputPath = '/tmp/RtmpCK1hIL/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpCK1hIL/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Attaching package: 'data.table'
The following object is masked from 'package:raster':
shift
Setting:
options(
spades.outputPath = '/tmp/RtmpMhWvQg/simOutputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpMhWvQg/reproducible/cache'
spades.inputPath = '/tmp/RtmpCK1hIL/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpMhWvQg/simOutputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
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
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-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = '/tmp/RtmpXuFsu6/reproducible/cache'
spades.inputPath = '/tmp/RtmpCK1hIL/SpaDES/inputs'
spades.outputPath = '/tmp/RtmpCK1hIL/SpaDES/outputs'
spades.modulePath = '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SpaDES.core/sampleModules'
)
Quitting from lines 205-215 (iii-cache.Rmd)
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
is.character(repoDir) & length(repoDir) == 1 is not TRUE
--- failed re-building ‘iii-cache.Rmd’
SUMMARY: processing the following file failed:
‘iii-cache.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-linux-x86_64
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: tests
Result: ERROR
Running 'test-all.R' [187s]
Flavor: r-oldrel-windows-ix86+x86_64
Version: 0.2.6
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
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/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpSOcAD1/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpYVgJw7/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpYVgJw7/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Setting:
options(
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpSOcAD1/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpYVgJw7/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpYVgJw7/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpSOcAD1/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpYVgJw7/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpYVgJw7/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Setting:
options(
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpSOcAD1/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpYVgJw7/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpYVgJw7/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Attaching package: 'data.table'
The following object is masked from 'package:raster':
shift
Setting:
options(
spades.outputPath = 'D:/temp/RtmpSOcAD1/simOutputs'
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpSOcAD1/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpYVgJw7/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpSOcAD1/simOutputs'
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
simList saved in
SpaDES.core:::.pkgEnv$.sim
It will be deleted at next spades call
Attaching package: 'magrittr'
The following object is masked from 'package:raster':
extract
Setting:
options(
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Paths set to:
options(
reproducible.cachePath = 'D:/temp/RtmpSOcAD1/reproducible/cache'
spades.inputPath = 'D:/temp/RtmpYVgJw7/SpaDES/inputs'
spades.outputPath = 'D:/temp/RtmpYVgJw7/SpaDES/outputs'
spades.modulePath = 'D:/temp/RtmpkDREEY/RLIBS_152c2113144a/SpaDES.core/sampleModules'
)
Quitting from lines 205-215 (iii-cache.Rmd)
Error: processing vignette 'iii-cache.Rmd' failed with diagnostics:
is.character(repoDir) & length(repoDir) == 1 is not TRUE
Execution halted
Flavor: r-oldrel-windows-ix86+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