* using log directory ‘/srv/hornik/tmp/CRAN_pretest/bootcluster.Rcheck’
* using R Under development (unstable) (2024-11-07 r87302)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.1 (1)
    Debian flang-new version 19.1.1 (1)
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘bootcluster/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bootcluster’ version ‘0.4.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [4s/4s] NOTE
Maintainer: ‘Tianmou Liu <tianmouliu@outlook.com>’

New maintainer:
  Tianmou Liu <tianmouliu@outlook.com>
Old maintainer(s):
  Tianmou Liu <tianmoul@buffalo.edu>

Possibly misspelled words in DESCRIPTION:
  Liu (28:22)

Package has a VignetteBuilder field but no prebuilt vignette index.
* checking package namespace information ... OK
* checking package dependencies ... INFO
Vignette dependency required without any vignettes: ‘knitr’
* 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 ‘bootcluster’ can be installed ... [5s/5s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... NOTE
Mismatches for apparent methods not registered:
min:
  function(..., na.rm)
min.agreement:
  function(clst, agrmt)
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] NOTE
calculate_smin_delta: no visible global function definition for
  ‘esmbl.stability’
create_consensus_graph: no visible global function definition for
  ‘graph_from_incidence_matrix’
create_consensus_graph: no visible global function definition for
  ‘set_graph_attr’
ensemble_clustering: no visible global function definition for
  ‘cluster_fast_greedy’
ensemble_clustering: no visible global function definition for ‘E’
extract_clustering: no visible global function definition for
  ‘membership’
plot_clustering_results: no visible global function definition for
  ‘prcomp’
plot_clustering_results: no visible binding for global variable ‘PC1’
plot_clustering_results: no visible binding for global variable ‘PC2’
plot_clustering_results: no visible binding for global variable
  ‘kmeans’
plot_clustering_results: no visible binding for global variable
  ‘hierarchical’
plot_clustering_results: no visible binding for global variable
  ‘spectral’
plot_clustering_results: no visible binding for global variable
  ‘ensemble’
plot_clustering_results: no visible binding for global variable
  ‘kmeans_stability’
plot_clustering_results: no visible binding for global variable
  ‘hierarchical_stability’
plot_clustering_results: no visible binding for global variable
  ‘spectral_stability’
plot_clustering_results: no visible global function definition for ‘E’
plot_smin_analysis: no visible binding for global variable ‘Method’
plot_smin_analysis: no visible binding for global variable ‘Value’
plot_smin_analysis: no visible binding for global variable ‘Type’
ref_dist: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  E Method PC1 PC2 Type Value cluster_fast_greedy ensemble
  esmbl.stability graph_from_incidence_matrix hierarchical
  hierarchical_stability kmeans kmeans_stability membership prcomp
  rnorm set_graph_attr spectral spectral_stability
Consider adding
  importFrom("stats", "kmeans", "prcomp", "rnorm")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [2s/2s] ERROR
  Running ‘test_ensemble.R’ [1s/1s]
Running the tests in ‘tests/test_ensemble.R’ failed.
Complete output:
  > # Test script for ensemble clustering functionality
  > 
  > library(bootcluster)
  > 
  > # Generate test data
  > set.seed(123)
  > n <- 150  # number of points
  > centers <- matrix(c(0,0, 2,2, -2,2), ncol=2, byrow=TRUE)
  > clusters <- sample(1:3, n, replace=TRUE)
  > x <- matrix(0, nrow=n, ncol=2)
  > for(i in 1:n) {
  +     x[i,] <- centers[clusters[i],] + rnorm(2, 0, 0.3)
  + }
  > 
  > # Test ensemble clustering with different k values
  > test_ensemble <- function() {
  +     # Test case 1: Equal k values
  +     res1 <- ensemble_clustering(x, k_km=3, k_hc=3, k_sc=3)
  +     cat("Test 1 - Equal k values:\n")
  +     cat("Number of clusters found:", length(unique(res1$membership)), "\n")
  +     cat("Modularity:", res1$modularity, "\n\n")
  +     
  +     # Test case 2: Different k values
  +     res2 <- ensemble_clustering(x, k_km=3, k_hc=4, k_sc=2)
  +     cat("Test 2 - Different k values:\n")
  +     cat("Number of clusters found:", length(unique(res2$membership)), "\n")
  +     cat("Modularity:", res2$modularity, "\n\n")
  +     
  +     # Test visualization
  +     plots <- plot_clustering_results(x, res1, pca=FALSE)
  +     print(plots$ensemble)
  +     
  +     # Test Smin analysis
  +     smin_plot <- plot_smin_analysis(res1)
  +     print(smin_plot)
  + }
  > 
  > # Run tests
  > test_ensemble()
  Error in ensemble_clustering(x, k_km = 3, k_hc = 3, k_sc = 3) : 
    could not find function "ensemble_clustering"
  Calls: test_ensemble
  Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 3 NOTEs