############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:omada.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings omada_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/omada.Rcheck' * using R Under development (unstable) (2023-01-10 r83596 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.2.0 GNU Fortran (GCC) 12.2.0 * running under: Windows Server x64 (build 20348) * 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 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 43.87 0.33 44.21 get_feature_selection_scores 40.86 0.20 41.07 get_partition_agreement_scores 31.75 0.09 31.85 get_signature_feature_coefs 29.60 0.22 29.89 get_sample_memberships 29.64 0.16 29.79 get_cluster_voting_memberships 29.47 0.24 29.70 get_cluster_voting_metric_votes 28.94 0.28 29.22 plot_partition_agreement 28.76 0.07 28.83 get_feature_selection_optimal_features 28.33 0.27 28.61 get_cluster_voting_k_votes 27.98 0.28 28.27 plot_signature_feature 28.08 0.18 28.28 get_cluster_voting_scores 28.07 0.09 28.20 plot_feature_selection 26.66 0.20 26.86 plot_cluster_voting 21.84 0.13 21.97 omada 20.30 0.11 20.48 get_optimal_features 10.34 0.06 10.41 get_optimal_memberships 10.06 0.03 10.09 plot_average_stabilities 9.38 0.03 9.41 get_optimal_stability_score 9.25 0.08 9.32 get_optimal_number_of_features 8.91 0.05 8.97 get_optimal_parameter_used 7.59 0.06 7.66 featureSelection 7.11 0.22 7.33 get_average_feature_k_stabilities 5.95 0.07 6.02 * 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 'F:/biocbuild/bbs-3.17-bioc/meat/omada.Rcheck/00check.log' for details.