* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/IPMRF.Rcheck’
* using R Under development (unstable) (2022-02-22 r81797)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘IPMRF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IPMRF’ version ‘1.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘randomForestSRC’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘IPMRF’ can be installed ... [13s/27s] OK
* checking package 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
* 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 ... [19s/30s] 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 examples ... [8s/12s] ERROR
Running examples in ‘IPMRF-Ex.R’ failed
The error most likely occurred in:

> ### Name: ipmparty
> ### Title: IPM casewise with CIT-RF by 'party' for OOB samples
> ### Aliases: ipmparty
> ### Keywords: tree multivariate
> 
> ### ** Examples
> 
> #Note: more examples can be found at 
> #https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1650-8
> 
> ## -------------------------------------------------------
> ## Example from \code{\link[party]{varimp}} in \pkg{party}
> ## Classification RF
> ## -------------------------------------------------------
> 
> ## Not run: 
> ##D library(party)
> ##D 
> ##D #from help in varimp by party package
> ##D set.seed(290875)
> ##D readingSkills.cf <- cforest(score ~ ., data = readingSkills,
> ##D control = cforest_unbiased(mtry = 2, ntree = 50))
> ##D 
> ##D # standard importance
> ##D varimp(readingSkills.cf)
> ##D 
> ##D # the same modulo random variation
> ##D varimp(readingSkills.cf, pre1.0_0 = TRUE)
> ##D 
> ##D # conditional importance, may take a while...
> ##D varimp(readingSkills.cf, conditional = TRUE)
> ## End(Not run)
> 
> #IMP based on CIT-RF (party package)
> library(party)
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: sandwich
> 
> ntree<-50
> #readingSkills: data from party package
> da<-readingSkills[,1:3] 
> set.seed(290875)
> readingSkills.cf3 <- cforest(score ~ ., data = readingSkills,
+ control = cforest_unbiased(mtry = 3, ntree = 50))
> 
> #IPM case-wise computed with OOB with party
> pupf<-ipmparty(readingSkills.cf3 ,da,ntree)
>  
> #global IPM
> pua<-apply(pupf,2,mean) 
> pua
nativeSpeaker           age      shoeSize 
 0.2689833248  0.7301704371  0.0008462381 
> 
> ## -------------------------------------------------------
> ## Example from \code{\link[randomForestSRC]{var.select}} in \pkg{randomForestSRC} 
> ## Multivariate mixed forests
> ## -------------------------------------------------------
> 
> ## Not run: 
> ##D library(randomForestSRC)
> ##D 
> ##D #from help in var.select by randomForestSRC package
> ##D mtcars.new <- mtcars
> ##D mtcars.new$cyl <- factor(mtcars.new$cyl)
> ##D mtcars.new$carb <- factor(mtcars.new$carb, ordered = TRUE)
> ##D mv.obj <- rfsrc(cbind(carb, mpg, cyl) ~., data = mtcars.new,
> ##D importance = TRUE)
> ##D var.select(mv.obj, method = "vh.vimp", nrep = 10) 
> ##D 
> ##D #different variables are selected if var.select is repeated 
> ##D 
> ## End(Not run)
> 
> #IMP based on CIT-RF (party package)
> library(randomForestSRC)
Error in library(randomForestSRC) : 
  there is no package called ‘randomForestSRC’
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/IPMRF.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 3:17.07, 104.66 + 10.27