* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/lnmCluster.Rcheck’
* using R Under development (unstable) (2025-11-17 r89032)
* 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 ‘lnmCluster/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lnmCluster’ version ‘0.3.1’
* 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 ‘lnmCluster’ can be installed ... [22s/18s] OK
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 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 ... [19s/19s] 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking examples with --run-donttest ... [30m/31m] ERROR
Running examples in ‘lnmCluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: lnmbiclust
> ### Title: Logistic Normal Multinomial Biclustering algorithm
> ### Aliases: lnmbiclust
> 
> ### ** Examples
> 
> #generate toy data with n=100, K=5,
> #set up parameters
> n<-100
> p<-5
> mu1<-c(-2.8,-1.3,-1.6,-3.9,-2.6)
> B1<-matrix(c(1,0,1,0,1,0,0,1,0,1),nrow = p, byrow=TRUE)
> T1<-diag(c(2.9,0.5))
> D1<-diag(c(0.52, 1.53, 0.56, 0.19, 1.32))
> cov1<-B1%*%T1%*%t(B1)+D1
> mu2<-c(1.5,-2.7,-1.1,-0.4,-1.4)
> B2<-matrix(c(1,0,1,0,0,1,0,1,0,1),nrow = p, byrow=TRUE)
> T2<-diag(c(0.2,0.003))
> D2<-diag(c(0.01, 0.62, 0.45, 0.01, 0.37))
> cov2<-B2%*%T2%*%t(B2)+D2
> 
> #generate normal distribution
> library(mvtnorm)
> simp<-rmultinom(n,1,c(0.6,0.4))
> lab<-as.factor(apply(t(simp),1,which.max))
> df<-matrix(0,nrow=n,ncol=p)
> for (i in 1:n) {
+  if(lab[i]==1){df[i,]<-rmvnorm(1,mu1,sigma = cov1)}
+  else if(lab[i]==2){df[i,]<-rmvnorm(1,mu2,sigma = cov2)}
+ }
> #apply inverse of additive log ratio and transform normal to count data
> f_df<-cbind(df,0)
> z<-exp(f_df)/rowSums(exp(f_df))
> W_count<-matrix(0,nrow=n,ncol=p+1)
> for (i in 1:n) {
+  W_count[i,]<-rmultinom(1,runif(1,10000,20000),z[i,])
+ }
> 
> #'#if run one model let range_Q be an integer
> ## No test: 
> res<-lnmbiclust(W_count,2,2,model="UUU")
Best model UUU G = 2 Q= 22
> ## End(No test)
> 
> #following will run 2 combinations of Q: 2 2, and 3 3 with G=2.
> ## No test: 
> res<-lnmbiclust(W_count,2,range_Q=c(2:3),model="UUU")
Best model UUU G = 2 Q= 22
> ## End(No test)
> 
> #if run model selection let range_Q and range_G be a vector.
> #model selection for all 16 models with G=1 to 3, Q=1 to 3.
> ## No test: 
> res<-lnmbiclust(W_count,c(1:3),c(1:3))
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [147s/150s]
 [147s/151s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [14s/14s] OK
* 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/lnmCluster.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 34:46.74, 2019.58 + 25.74