* using log directory ‘/srv/hornik/tmp/CRAN_pretest/Silhouette.Rcheck’ * using R Under development (unstable) (2025-06-17 r88325) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 19.1.7 (3) Debian flang-new version 19.1.7 (3) * running under: Debian GNU/Linux 13 (trixie) * using session charset: UTF-8 * checking for file ‘Silhouette/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Silhouette’ version ‘0.9’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [3s/5s] NOTE Maintainer: ‘Shrikrishna Bhat K’ New submission Possibly misspelled words in DESCRIPTION: biclustering (16:43) Package has a VignetteBuilder field but no prebuilt vignette index. Found the following URLs which should use \doi (with the DOI name only): File ‘Silhouette.Rd’: https://doi.org/10.1016/0377-0427(87)90125-7 https://doi.org/10.1080/0094965031000136012 https://doi.org/10.1080/10618600.2022.2050249 https://doi.org/10.1016/j.fss.2006.07.006 https://doi.org/10.1080/23737484.2024.2408534 File ‘extSilhouette.Rd’: https://doi.org/10.1007/s00357-008-9005-9 File ‘plot.Silhouette.Rd’: https://doi.org/10.1016/0377-0427(87)90125-7 https://doi.org/10.1080/0094965031000136012 https://doi.org/10.1080/10618600.2022.2050249 https://doi.org/10.1016/j.fss.2006.07.006 https://doi.org/10.1007/s00357-008-9005-9 File ‘softSilhouette.Rd’: https://doi.org/10.1080/10618600.2022.2050249 https://doi.org/10.1080/23737484.2024.2408534 * 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 serialization versions ... OK * checking whether package ‘Silhouette’ can be installed ... [3s/3s] OK * checking package directory ... OK * checking for future file timestamps ... OK * checking DESCRIPTION meta-information ... NOTE Maintainer field differs from that derived from Authors@R Maintainer: ‘Shrikrishna Bhat K’ Authors@R: ‘Shrikrishna Bhat K ’ * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [4s/4s] NOTE Silhouette: no visible global function definition for ‘isGeneric’ Silhouette: no visible global function definition for ‘getMethod’ Silhouette: no visible global function definition for ‘slotNames’ Silhouette: no visible global function definition for ‘slot’ plot.Silhouette: no visible binding for global variable ‘cluster’ plot.Silhouette: no visible binding for global variable ‘sil_width’ plot.Silhouette: no visible binding for global variable ‘original_name’ plot.Silhouette: no visible binding for global variable ‘name’ softSilhouette: no visible global function definition for ‘isGeneric’ softSilhouette: no visible global function definition for ‘getMethod’ softSilhouette: no visible global function definition for ‘slotNames’ softSilhouette: no visible global function definition for ‘slot’ Undefined global functions or variables: cluster getMethod isGeneric name original_name sil_width slot slotNames Consider adding importFrom("methods", "getMethod", "isGeneric", "slot", "slotNames") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 examples ... [11s/11s] ERROR Running examples in ‘Silhouette-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: extSilhouette > ### Title: Calculate Extended Silhouette Width for Multi-Way Clustering > ### Aliases: extSilhouette > > ### ** Examples > > # Example using iris dataset with two modes > data(iris) > if (requireNamespace("ppclust", quietly = TRUE)) { + library(ppclust) + # Mode 1: Crisp silhouette with kmeans + kmeans_res <- kmeans(iris[, 1:4], centers = 3) + dist_mat <- as.matrix(dist(rbind(kmeans_res$centers, + iris[, 1:4])))[-(1:3), 1:3] + sil_mode1 <- Silhouette( + prox_matrix = dist_mat, + print.summary = FALSE + ) + + # Mode 2: Fuzzy silhouette with fcm + sil_mode2 <- Silhouette( + prox_matrix = "d", + proximity_type = "dissimilarity", + prob_matrix = "u", + clust_fun = ppclust::fcm, + x = t(iris[, 1:4]), + centers = 2, + print.summary = FALSE + ) + + # Extended silhouette + ext_sil <- extSilhouette(list(sil_mode1, sil_mode2)) + } else { + message("Install 'ppclust': install.packages('ppclust')") + } --------------------------- Extended silhouette: 0.6725 --------------------------- Dimension Summary: dimension n_obs avg_sil_width 1 Mode 1 150 0.6664 2 Mode 2 4 0.9027 Available components: [1] "ext_sil_width" "dim_table" > > if (requireNamespace("blockcluster", quietly = TRUE)) { + library(blockcluster) + result <- coclusterContinuous( + as.matrix(iris[, -5]), + nbcocluster = c(3, 2) + ) + sil_mode1 <- softSilhouette( + prob_matrix = result@rowposteriorprob, + method = "pac", + print.summary = FALSE + ) + sil_mode2 <- softSilhouette( + prob_matrix = result@colposteriorprob, + method = "pac", + print.summary = FALSE + ) + + # Extended silhouette + ext_sil <- extSilhouette(list(sil_mode1, sil_mode2)) + } else { + message("Install 'blockcluster': install.packages('blockcluster')") + } Loading required package: rtkore Loading required package: Rcpp Attaching package: ‘rtkore’ The following object is masked from ‘package:Rcpp’: LdFlags blockcluster version 4.5.5 loaded ---------------- Copyright (C) Please post questions and bugs at: Co-Clustering Failed! Error in softSilhouette(prob_matrix = result@rowposteriorprob, method = "pac", : When clust_fun is NULL, prob_matrix must be a numeric matrix. Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed Silhouette 10.091 0.048 10.145 * checking PDF version of manual ... [2s/2s] 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, 4 NOTEs