############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:DuoClustering2018.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings DuoClustering2018_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/DuoClustering2018.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘DuoClustering2018/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DuoClustering2018’ version ‘1.25.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘DuoClustering2018’ can be installed ... OK * checking installed package size ... OK * 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 whether startup messages can be suppressed ... 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 ari_df: no visible binding for global variable ‘cell’ plot_entropy: no visible binding for global variable ‘dataset’ plot_entropy: no visible binding for global variable ‘method’ plot_entropy: no visible binding for global variable ‘run’ plot_entropy: no visible binding for global variable ‘k’ plot_entropy: no visible binding for global variable ‘cluster’ plot_entropy: no visible binding for global variable ‘trueclass’ plot_entropy: no visible binding for global variable ‘s’ plot_entropy: no visible binding for global variable ‘s.true’ plot_entropy: no visible binding for global variable ‘est_k’ plot_entropy: no visible binding for global variable ‘sce’ plot_entropy: no visible binding for global variable ‘filtering’ plot_entropy: no visible binding for global variable ‘truenclust’ plot_entropy: no visible binding for global variable ‘entropy’ plot_entropy: no visible binding for global variable ‘ARI’ plot_entropy: no visible binding for global variable ‘s.norm’ plot_entropy: no visible binding for global variable ‘s.true.norm’ plot_entropy: no visible binding for global variable ‘ds’ plot_entropy: no visible binding for global variable ‘ds.norm’ plot_k_diff: no visible binding for global variable ‘dataset’ plot_k_diff: no visible binding for global variable ‘method’ plot_k_diff: no visible binding for global variable ‘run’ plot_k_diff: no visible binding for global variable ‘k’ plot_k_diff: no visible binding for global variable ‘cluster’ plot_k_diff: no visible binding for global variable ‘trueclass’ plot_k_diff: no visible binding for global variable ‘est_k’ plot_k_diff: no visible binding for global variable ‘elapsed’ plot_k_diff: no visible binding for global variable ‘sce’ plot_k_diff: no visible binding for global variable ‘filtering’ plot_k_diff: no visible binding for global variable ‘truenclust’ plot_k_diff: no visible binding for global variable ‘ARI’ plot_k_diff: no visible binding for global variable ‘medARI’ plot_k_diff: no visible binding for global variable ‘k_diff’ plot_k_diff: no visible binding for global variable ‘estnclust’ plot_performance: no visible binding for global variable ‘dataset’ plot_performance: no visible binding for global variable ‘method’ plot_performance: no visible binding for global variable ‘run’ plot_performance: no visible binding for global variable ‘k’ plot_performance: no visible binding for global variable ‘cluster’ plot_performance: no visible binding for global variable ‘trueclass’ plot_performance: no visible binding for global variable ‘est_k’ plot_performance: no visible binding for global variable ‘elapsed’ plot_performance: no visible binding for global variable ‘sce’ plot_performance: no visible binding for global variable ‘filtering’ plot_performance: no visible binding for global variable ‘ARI’ plot_performance: no visible binding for global variable ‘truenclust’ plot_performance: no visible binding for global variable ‘medianARI’ plot_performance: no visible binding for global variable ‘estnclust’ plot_stability: no visible binding for global variable ‘dataset’ plot_stability: no visible binding for global variable ‘method’ plot_stability: no visible binding for global variable ‘k’ plot_stability: no visible binding for global variable ‘data.wide’ plot_stability: no visible binding for global variable ‘stability’ plot_stability: no visible binding for global variable ‘truenclust’ plot_stability: no visible binding for global variable ‘sce’ plot_stability: no visible binding for global variable ‘filtering’ plot_stability: no visible binding for global variable ‘ari.stab’ plot_stability: no visible binding for global variable ‘median.stability’ plot_timing: no visible binding for global variable ‘dataset’ plot_timing: no visible binding for global variable ‘method’ plot_timing: no visible binding for global variable ‘run’ plot_timing: no visible binding for global variable ‘k’ plot_timing: no visible binding for global variable ‘cluster’ plot_timing: no visible binding for global variable ‘trueclass’ plot_timing: no visible binding for global variable ‘est_k’ plot_timing: no visible binding for global variable ‘elapsed’ plot_timing: no visible binding for global variable ‘sce’ plot_timing: no visible binding for global variable ‘filtering’ plot_timing: no visible binding for global variable ‘truenclust’ plot_timing: no visible binding for global variable ‘median.elapsed’ plot_timing: no visible binding for global variable ‘med.t’ plot_timing: no visible binding for global variable ‘norm.time’ plot_timing: no visible binding for global variable ‘medianelapsed’ Undefined global functions or variables: ARI ari.stab cell cluster data.wide dataset ds ds.norm elapsed entropy est_k estnclust filtering k k_diff med.t medARI median.elapsed median.stability medianARI medianelapsed method norm.time run s s.norm s.true s.true.norm sce stability trueclass truenclust * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed sce_full_Koh 4.694 0.214 5.076 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.21-data-experiment/meat/DuoClustering2018.Rcheck/00check.log’ for details.