############################################################################## ############################################################################## ### ### 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_1.7.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/ClustIRR.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ClustIRR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClustIRR’ version ‘1.7.1’ * 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.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_summary: no visible binding for global variable ‘community’ get_beta_scatterplot : get_scatters: no visible binding for global variable ‘mean_x’ get_beta_scatterplot : get_scatters: no visible binding for global variable ‘mean_y’ get_beta_scatterplot : get_scatters: no visible binding for global variable ‘specificity’ get_beta_scatterplot : get_scatters: no visible binding for global variable ‘size_x’ get_beta_scatterplot : get_scatters: no visible binding for global variable ‘size_y’ get_beta_scatterplot: no visible binding for global variable ‘community’ get_beta_violins : get_violins: no visible binding for global variable ‘specificity’ get_beta_violins : get_violins: no visible binding for global variable ‘size’ get_beta_violins: no visible binding for global variable ‘community’ 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.. community mean_x mean_y size size_x size_y specificity x_adj y_adj * checking Rd files ... NOTE prepare_Rd: decode_communities.Rd:21-23: Dropping empty section \details * 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 ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_beta_violins 60.138 2.793 62.408 get_beta_scatterplot 60.068 2.585 62.211 get_ag_summary 60.012 2.618 62.191 dco 59.581 2.016 61.647 detect_communities 5.220 0.658 5.477 decode_communities 5.235 0.521 5.469 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/ClustIRR.Rcheck/00check.log’ for details.