* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/RHclust.Rcheck’
* using R Under development (unstable) (2025-11-16 r89026)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
    GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘RHclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RHclust’ version ‘2.0.0’
* package encoding: UTF-8
* 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 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 ‘RHclust’ can be installed ... 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 code 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 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 ... [13s/16s] 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 ... OK
* checking examples with --run-donttest ... [30m/34m] ERROR
Running examples in ‘RHclust-Ex.R’ failed
The error most likely occurred in:

> ### Name: VIPcov
> ### Title: Vector in Partition with covariates
> ### Aliases: VIPcov
> 
> ### ** Examples
> 
> ## No test: 
> ## simple output of 3 clusters assignments
> sd = SimData(1, g = 36, c(33,33,34))
> VIPout = VIPcov(sd, v = 3, covariates = sd$Covariates)
> 
> # loop through clusters 1-10 and outputs plot of WSS, AIC, and BIC
> VIPout = VIPcov(sd, v = c(1,10), covariates = sd$Covariates)
Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  5 initial clusters reduced to 3

Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  6 initial clusters reduced to 5

Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  7 initial clusters reduced to 5

Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  8 initial clusters reduced to 4

Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  9 initial clusters reduced to 5

Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  10 initial clusters reduced to 3

Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  Total WSS clusters have been labeled based on assigned number of centers.
Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  AIC clusters have been labeled based on assigned number of centers.
Warning in VIPcov(sd, v = c(1, 10), covariates = sd$Covariates) :
  BIC clusters have been labeled based on assigned number of centers.
> 
> # loop through clusters 1-10 but picks first instance of increasing slope
> VIPout = VIPcov(sd, v = c(1,10), optimize = 'slope', covariates = sd$Covariates)
Warning in VIPcov(sd, v = c(1, 10), optimize = "slope", covariates = sd$Covariates) :
  4 initial clusters reduced to 3

> 
> 
> # Individual inputs
> sd = SimData(1, g = 36, k = c(33,33,34))
> VIPout = VIPcov(SNP = sd$SNP, CPG = sd$CPG, GE = sd$GE,
+             SNPname = sd$SNP_Index, CPGname = sd$CPG_Index,
+             GEname = sd$GE_Index,
+             v = c(1,5), optimize = 'off', nstart = 5, covariates = sd$Covariates)
Warning in VIPcov(SNP = sd$SNP, CPG = sd$CPG, GE = sd$GE, SNPname = sd$SNP_Index,  :
  5 initial clusters reduced to 4

Warning in VIPcov(SNP = sd$SNP, CPG = sd$CPG, GE = sd$GE, SNPname = sd$SNP_Index,  :
  Total WSS clusters have been labeled based on assigned number of centers.
Warning in VIPcov(SNP = sd$SNP, CPG = sd$CPG, GE = sd$GE, SNPname = sd$SNP_Index,  :
  AIC clusters have been labeled based on assigned number of centers.
Warning in VIPcov(SNP = sd$SNP, CPG = sd$CPG, GE = sd$GE, SNPname = sd$SNP_Index,  :
  BIC clusters have been labeled based on assigned number of centers.
> 
> 
> ## Varying clusters
> sd = SimData(k = c(10,40,50))
> out = VIPcov(sd, v = c(1,6), optimize = 'elbow', nstart = 30, covariates = sd$Covariates)
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/RHclust.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 34:36.03, 1820.79 + 12.61