CRAN Package Check Results for Package SpaDES.core

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

Check Details

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