############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClustIRR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClustIRR_1.9.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/ClustIRR.Rcheck’ * using R Under development (unstable) (2025-11-04 r88984) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.8 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ClustIRR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClustIRR’ version ‘1.9.1’ * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ClustIRR’ can be installed ... OK * used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.1.sdk’ * checking C++ specification ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘ggplot2’ A package should be listed in only one of these fields. * 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 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 ... NOTE get_ag_gene_hits: no visible binding for global variable ‘cells’ get_ag_gene_hits: no visible binding for global variable ‘clones’ get_ag_gene_hits: no visible binding for global variable ‘community’ get_ag_gene_hits: no visible binding for global variable ‘ag’ get_ag_species_hits: no visible binding for global variable ‘cells’ get_ag_species_hits: no visible binding for global variable ‘clones’ get_ag_species_hits: no visible binding for global variable ‘community’ get_ag_species_hits: no visible binding for global variable ‘ag’ get_beta_violin: no visible binding for global variable ‘spec’ get_beta_violin: no visible binding for global variable ‘size’ get_cosine_similarity: no visible binding for global variable ‘CS’ get_honeycombs: no visible binding for global variable ‘x_adj’ get_honeycombs: no visible binding for global variable ‘y_adj’ get_honeycombs: no visible binding for global variable ‘..count..’ Undefined global functions or variables: ..count.. CS ag cells clones community size spec x_adj y_adj * checking Rd files ... OK * checking Rd metadata ... 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 ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... INFO GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... INFO Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘ClustIRR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: get_cosine_similarity > ### Title: Compute and Visualize Cosine Similarity (CS) > ### Aliases: get_cosine_similarity > > ### ** Examples > > # Create a sample matrix > mat <- matrix(rpois(n=30, lambda = 4), nrow = 5, + dimnames = list(NULL, c("A", "B", "C"))) Error in matrix(rpois(n = 30, lambda = 4), nrow = 5, dimnames = list(NULL, : length of 'dimnames' [2] not equal to array extent Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_beta_violin 105.578 6.125 117.538 dco 106.006 5.022 117.150 decode_all_communities 9.262 0.863 10.318 get_ag_gene_hits 5.590 1.177 6.424 decode_community 5.779 0.800 6.402 detect_communities 5.795 0.781 6.216 get_ag_species_hits 5.537 0.876 6.328 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/Users/biocbuild/bbs-3.23-bioc/meat/ClustIRR.Rcheck/00check.log’ for details.