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* using log directory 'd:/RCompile/CRANincoming/R-devel/epicontacts.Rcheck'
* using R Under development (unstable) (2017-05-09 r72665)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'epicontacts/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'epicontacts' version '1.0.1'
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: 'VP Nagraj <[email protected]>'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'epicontacts' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
** checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'epicontacts-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.igraph.epicontacts
> ### Title: Create igraph object from contact data
> ### Aliases: as.igraph.epicontacts
> 
> ### ** Examples
> 
> 
> if (require(outbreaks) && require(igraph)) {
+ ## build data
+ 
+ x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
+                       id = "case.id", to = "case.id", from ="infector",
+                       directed = TRUE)
+ 
+ 
+ ## subset data - keep 50 cases from linelist with contacts
+ 
+ ids <- get_id(x, "common")[1:50]
+ ids
+ x <- x[ids, ids]
+ 
+ 
+ ## make igraph object with associated attributes from epicontacts object
+ 
+ net <- as.igraph(x)
+ net
+ plot(net, vertex.label = "", vertex.size = 10,
+      vertex.color = cases_pal(50))
+ }
Loading required package: outbreaks
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Error in `[.data.frame`(linelist, , id) : undefined columns selected
Calls: make_epicontacts -> [ -> [.data.frame
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'epicontacts-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.igraph.epicontacts
> ### Title: Create igraph object from contact data
> ### Aliases: as.igraph.epicontacts
> 
> ### ** Examples
> 
> 
> if (require(outbreaks) && require(igraph)) {
+ ## build data
+ 
+ x <- make_epicontacts(ebola_sim$linelist, ebola_sim$contacts,
+                       id = "case.id", to = "case.id", from ="infector",
+                       directed = TRUE)
+ 
+ 
+ ## subset data - keep 50 cases from linelist with contacts
+ 
+ ids <- get_id(x, "common")[1:50]
+ ids
+ x <- x[ids, ids]
+ 
+ 
+ ## make igraph object with associated attributes from epicontacts object
+ 
+ net <- as.igraph(x)
+ net
+ plot(net, vertex.label = "", vertex.size = 10,
+      vertex.color = cases_pal(50))
+ }
Loading required package: outbreaks
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Error in `[.data.frame`(linelist, , id) : undefined columns selected
Calls: make_epicontacts -> [ -> [.data.frame
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ... [3s] ERROR
  Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1: make_epicontacts(ebola_sim$linelist, ebola_sim$contacts, id = "case.id", to = "case.id", 
         from = "infector", directed = TRUE) at testthat/test_thin.R:4
  2: linelist[, id]
  3: `[.data.frame`(linelist, , id)
  4: stop("undefined columns selected")
  
  testthat results ================================================================
  OK: 0 SKIPPED: 36 FAILED: 4
  1. Error: Various subsetting using [ (@test_handling.R#4) 
  2. Error: Errors / warnings happen when they should (@test_handling.R#55) 
  3. Error: Reordering of columns works (@test_make_epicontacts.R#85) 
  4. Error: Thin ouputs are correct (@test_thin.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
** running tests for arch 'x64' ... [2s] ERROR
  Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1: make_epicontacts(ebola_sim$linelist, ebola_sim$contacts, id = "case.id", to = "case.id", 
         from = "infector", directed = TRUE) at testthat/test_thin.R:4
  2: linelist[, id]
  3: `[.data.frame`(linelist, , id)
  4: stop("undefined columns selected")
  
  testthat results ================================================================
  OK: 0 SKIPPED: 36 FAILED: 4
  1. Error: Various subsetting using [ (@test_handling.R#4) 
  2. Error: Errors / warnings happen when they should (@test_handling.R#55) 
  3. Error: Reordering of columns works (@test_make_epicontacts.R#85) 
  4. Error: Thin ouputs are correct (@test_thin.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [10s] WARNING
Error in re-building vignettes:
  ...
Warning in structure(x, class = unique(c("AsIs", oldClass(x)))) :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Quitting from lines 219-233 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
undefined columns selected
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 4 ERRORs, 1 WARNING

Warning in structure(x, class = unique(c("AsIs", oldClass(x)))) :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.