############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ClassifyR_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ClassifyR.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ClassifyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClassifyR’ version ‘2.14.0’ * checking package namespace information ... OK * checking package dependencies ... 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 ‘ClassifyR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘MultiAssayExperiment’ A package should be listed in only one of these fields. * checking top-level files ... OK * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .posterior_probs : : no visible global function definition for ‘dmvnorm’ easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no visible binding for global variable ‘measurements’ kTSPclassifier,DataFrame : : no visible global function definition for ‘Pairs’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘measurement’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘..density..’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘legends grouping’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘key’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘value’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘ID’ rankingPlot,list : : : no visible global function definition for ‘first’ rankingPlot,list : : : no visible global function definition for ‘second’ rankingPlot,list : : : : no visible global function definition for ‘first’ rankingPlot,list : : : : no visible global function definition for ‘second’ runTest,DataFrame: no visible binding for global variable ‘setsNodes’ runTestEasyHard,MultiAssayExperiment: no visible binding for global variable ‘setsNodes’ runTests,DataFrame: no visible global function definition for ‘mcols’ runTests,DataFrame: no visible binding for global variable ‘setsNodes’ runTests,DataFrame: no visible binding for global variable ‘dataset’ runTests,DataFrame : : no visible global function definition for ‘mcols’ runTests,DataFrame : : no visible global function definition for ‘mcols<-’ runTests,DataFrame: no visible global function definition for ‘mcols<-’ runTestsEasyHard,MultiAssayExperiment: no visible binding for global variable ‘setsNodes’ runTestsEasyHard,MultiAssayExperiment: no visible binding for global variable ‘.iteration’ samplesMetricMap,list: no visible binding for global variable ‘Class’ samplesMetricMap,list: no visible binding for global variable ‘Group’ samplesMetricMap,list: no visible binding for global variable ‘measurements’ samplesMetricMap,list: no visible binding for global variable ‘name’ samplesMetricMap,list: no visible binding for global variable ‘type’ samplesMetricMap,list: no visible binding for global variable ‘Metric’ samplesMetricMap,matrix: no visible binding for global variable ‘Class’ samplesMetricMap,matrix: no visible binding for global variable ‘Group’ samplesMetricMap,matrix: no visible binding for global variable ‘measurements’ samplesMetricMap,matrix: no visible binding for global variable ‘name’ samplesMetricMap,matrix: no visible binding for global variable ‘type’ samplesMetricMap,matrix: no visible binding for global variable ‘Metric’ selectionPlot,list : : : no visible global function definition for ‘first’ selectionPlot,list : : : no visible global function definition for ‘second’ selectionPlot,list : : : : no visible global function definition for ‘first’ selectionPlot,list : : : : no visible global function definition for ‘second’ selectionPlot,list: no visible binding for global variable ‘Freq’ Undefined global functions or variables: ..density.. .iteration Class Freq Group ID Metric Pairs dataset dmvnorm first key legends grouping mcols mcols<- measurement measurements name second setsNodes type value Consider adding importFrom("base", "grouping") 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 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 ClassifyResult-class 55.493 2.937 20.719 elasticNetFeatures 21.860 1.937 9.176 runTests 15.632 4.027 6.956 DLDAinterface 18.359 0.962 0.084 elasticNetGLMinterface 14.006 1.587 9.830 distribution 11.297 2.072 5.827 previousTrained 6.018 3.782 4.752 DMDselection 5.966 0.172 6.139 previousSelection 3.623 2.018 4.874 ROCplot 5.083 0.164 5.247 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/ClassifyR.Rcheck/00check.log’ for details.