############################################################################## ############################################################################## ### ### 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-rtools43/meat/omada.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * 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 40.00 0.17 40.17 get_feature_selection_scores 38.96 0.24 39.20 get_partition_agreement_scores 31.49 0.26 31.75 get_sample_memberships 28.37 0.19 28.58 get_cluster_voting_memberships 27.13 0.11 27.23 get_cluster_voting_scores 27.03 0.11 27.14 get_feature_selection_optimal_features 26.55 0.17 26.72 get_cluster_voting_metric_votes 26.25 0.23 26.49 get_cluster_voting_k_votes 25.68 0.25 25.94 plot_signature_feature 24.74 0.12 24.88 plot_partition_agreement 24.44 0.16 24.59 plot_feature_selection 24.15 0.09 24.27 get_signature_feature_coefs 23.60 0.19 23.79 omada 18.30 0.12 18.42 plot_cluster_voting 18.06 0.17 18.24 get_optimal_number_of_features 9.32 0.08 9.39 get_optimal_features 8.79 0.08 8.88 plot_average_stabilities 8.31 0.02 8.33 get_optimal_stability_score 7.42 0.06 7.49 featureSelection 7.09 0.13 7.22 get_optimal_parameter_used 7.12 0.02 7.15 get_optimal_memberships 6.27 0.01 6.28 * 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-rtools43/meat/omada.Rcheck/00check.log' for details.