############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:omada.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings omada_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/omada.Rcheck’ * using R Under development (unstable) (2023-02-14 r83833) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 * running under: Ubuntu 20.04.6 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... 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 plot_feature_selection 39.913 2.819 112.997 get_feature_selection_scores 41.162 0.028 41.190 get_feature_selection_optimal_number_of_features 40.415 0.104 40.519 plot_partition_agreement 30.765 9.320 62.667 plot_signature_feature 24.269 14.491 83.370 plot_cluster_voting 36.756 0.108 69.264 get_signature_feature_coefs 32.239 0.088 32.398 get_partition_agreement_scores 32.059 0.120 32.180 get_cluster_voting_k_votes 30.684 0.088 30.772 get_sample_memberships 29.531 0.040 29.939 get_cluster_voting_memberships 28.736 0.024 28.761 get_cluster_voting_metric_votes 27.623 0.080 27.703 get_cluster_voting_scores 27.435 0.036 27.471 get_feature_selection_optimal_features 26.134 0.032 26.167 omada 24.225 0.052 24.285 plot_average_stabilities 15.804 0.008 19.109 get_optimal_number_of_features 10.532 0.000 10.532 get_optimal_features 9.452 0.060 9.513 get_optimal_parameter_used 8.051 0.044 8.096 get_optimal_stability_score 8.081 0.004 8.085 get_optimal_memberships 7.583 0.000 7.583 featureSelection 7.324 0.123 7.448 get_average_feature_k_stabilities 5.855 0.064 5.920 * 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 ... ‘omada-vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/omada.Rcheck/00check.log’ for details.