############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:omada.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings omada_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/omada.Rcheck’ * using R Under development (unstable) (2023-01-10 r83596) * using platform: x86_64-apple-darwin17.0 (64-bit) * R was compiled by Apple clang version 12.0.0 (clang-1200.0.32.29) GNU Fortran (GCC) 8.2.0 * running under: macOS Mojave 10.14.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘omada/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘omada’ version ‘1.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'pdfCluster', 'kernlab', 'fpc', 'Rcpp', 'diceR', 'ggplot2', 'reshape', 'clusterCrit', 'clValid', 'glmnet', 'dplyr' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘omada’ 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 ... 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 R 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 ... NOTE Packages in Depends field not imported from: ‘Rcpp’ ‘clusterCrit’ ‘glmnet’ ‘kernlab’ ‘reshape’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE clusterVoting: no visible binding for global variable ‘k’ clusterVoting: no visible binding for global variable ‘Frequency’ clusteringMethodSelection: no visible binding for global variable ‘value’ clusteringMethodSelection: no visible binding for global variable ‘methods’ featureSelection: no visible binding for global variable ‘featureSet’ featureSelection: no visible binding for global variable ‘means’ geneSignatures: no visible global function definition for ‘where’ geneSignatures: no visible binding for global variable ‘features’ geneSignatures: no visible binding for global variable ‘value’ geneSignatures: no visible binding for global variable ‘variable’ Undefined global functions or variables: Frequency featureSet features k means methods value variable where Consider adding importFrom("utils", "methods") to your NAMESPACE file. * 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed get_feature_selection_optimal_number_of_features 74.438 0.243 95.942 get_feature_selection_scores 73.088 0.273 94.069 plot_partition_agreement 51.198 0.180 68.082 get_cluster_voting_metric_votes 50.885 0.190 65.875 get_partition_agreement_scores 50.195 0.168 66.554 plot_feature_selection 49.898 0.214 81.566 get_signature_feature_coefs 49.152 0.178 81.975 get_sample_memberships 49.035 0.144 65.595 get_feature_selection_optimal_features 48.951 0.151 62.450 get_cluster_voting_k_votes 48.819 0.184 66.697 plot_signature_feature 48.312 0.166 65.423 get_cluster_voting_memberships 48.175 0.158 62.131 get_cluster_voting_scores 47.955 0.158 60.811 omada 38.648 0.197 84.834 plot_cluster_voting 36.236 0.231 79.295 get_optimal_features 17.209 0.056 24.549 plot_average_stabilities 16.233 0.137 35.085 get_optimal_number_of_features 16.160 0.046 22.247 get_optimal_parameter_used 15.302 0.038 20.967 get_optimal_memberships 14.793 0.041 21.077 get_optimal_stability_score 14.741 0.053 19.997 featureSelection 11.928 0.051 16.306 get_average_feature_k_stabilities 8.804 0.047 11.957 get_generated_dataset 6.039 0.017 7.960 feasibilityAnalysisDataBased 4.974 0.069 6.633 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... 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-3.17-bioc/meat/omada.Rcheck/00check.log’ for details.