############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ClassifyR_3.0.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ClassifyR.Rcheck’ * using R version 4.2.1 (2022-06-23) * 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 ‘3.0.3’ * package encoding: UTF-8 * 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 ... NOTE Found the following hidden files and directories: dump/.-package.R These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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 ... OK * 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 .doSelection : : no visible binding for global variable ‘trainParams’ .doSelection : : no visible binding for global variable ‘predictParams’ .doSelection : : no visible binding for global variable ‘classesTrain’ .doSelection : : no visible binding for global variable ‘measurementsSubset’ .doSelection : : no visible binding for global variable ‘aResult’ .doTrain : : no visible binding for global variable ‘crossValParams’ .doTrain : : no visible binding for global variable ‘performanceName’ .doTrain: no visible binding for global variable ‘performanceType’ .getFeaturesStrings : : no visible global function definition for ‘first’ .getFeaturesStrings : : no visible global function definition for ‘second’ .posterior_probs : : no visible global function definition for ‘dmvnorm’ .samplesSplits : : no visible binding for global variable ‘classes’ .splitDataAndOutcomes: no visible binding for global variable ‘classColumn’ .splitDataAndOutcomes: no visible global function definition for ‘mcols<-’ elasticNetPreval: no visible binding for global variable ‘elasticNetGLMtrainInterfacePreval’ generateModellingParams: no visible global function definition for ‘kNNparams’ logisticParams: no visible binding for global variable ‘logisticTrainInterface’ logisticParams: no visible binding for global variable ‘logisticPredictInterface’ KolmogorovSmirnovRanking,MultiAssayExperiment: no visible binding for global variable ‘dataTable’ KullbackLeiblerRanking,MultiAssayExperiment: no visible binding for global variable ‘dataTable’ PredictParams,functionOrNULL: no visible global function definition for ‘DataFrame’ ROCplot,list : : no visible binding for global variable ‘FPR’ ROCplot,list : : no visible binding for global variable ‘TPR’ ROCplot,list : : no visible binding for global variable ‘lower’ ROCplot,list : : no visible binding for global variable ‘upper’ SelectParams,functionOrList: no visible global function definition for ‘DataFrame’ TrainParams,function: no visible global function definition for ‘DataFrame’ crossValidate,data.frame: no visible global function definition for ‘mcols<-’ crossValidate,list : : no visible global function definition for ‘mcols<-’ crossValidate,matrix: no visible global function definition for ‘mcols<-’ distribution,ClassifyResult: no visible binding for global variable ‘allPredictions’ distribution,ClassifyResult: no visible global function definition for ‘first’ distribution,ClassifyResult: no visible global function definition for ‘second’ distribution,ClassifyResult: no visible global function definition for ‘mcols<-’ elasticNetGLMpredictInterface,multnet-matrix: no visible global function definition for ‘DataFrame’ fisherDiscriminant,MultiAssayExperiment: no visible binding for global variable ‘measurements’ fisherDiscriminant,matrix: no visible global function definition for ‘DataFrame’ kTSPclassifier,DataFrame : : no visible global function definition for ‘Pairs’ kTSPclassifier,MultiAssayExperiment: no visible binding for global variable ‘measurementsTest’ naiveBayesKernel,DataFrame: no visible binding for global variable ‘weight’ naiveBayesKernel,DataFrame: no visible binding for global variable ‘test’ naiveBayesKernel,MultiAssayExperiment: no visible binding for global variable ‘measurements’ pcaPredictInterface,pcaModel-DFrame: no visible global function definition for ‘mcols<-’ pcaTrainInterface,DFrame: no visible global function definition for ‘mcols<-’ 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’ prevalPredictInterface,prevalModel-DFrame: no visible global function definition for ‘mcols<-’ prevalTrainInterface,DFrame: no visible global function definition for ‘mcols<-’ rankingPlot,list: no visible binding for global variable ‘top’ rankingPlot,list: no visible binding for global variable ‘overlap’ runTest,DataFrame: no visible global function definition for ‘DataFrame’ runTest,MultiAssayExperiment: no visible binding for global variable ‘measurements’ 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 binding for global variable ‘overlap’ selectionPlot,list : : no visible binding for global variable ‘feature’ selectionPlot,list: no visible binding for global variable ‘feature’ selectionPlot,list: no visible binding for global variable ‘colourVariable’ selectionPlot,list: no visible binding for global variable ‘size’ selectionPlot,list: no visible binding for global variable ‘Freq’ Undefined global functions or variables: ..density.. Class DataFrame FPR Freq Group ID Metric Pairs TPR aResult allPredictions classColumn classes classesTrain colourVariable crossValParams dataTable dmvnorm elasticNetGLMtrainInterfacePreval feature first kNNparams key legends grouping logisticPredictInterface logisticTrainInterface lower mcols<- measurement measurements measurementsSubset measurementsTest name overlap performanceName performanceType predictParams second size test top trainParams type upper value weight 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 crossValidate 372.865 2.226 375.102 ClassifyResult-class 107.189 5.579 32.306 elasticNetFeatures 24.244 2.371 11.103 elasticNetGLM 22.485 2.296 9.625 distribution 13.588 1.576 5.707 runTests 10.696 1.560 4.771 * 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-3.15-bioc/meat/ClassifyR.Rcheck/00check.log’ for details.