############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ClassifyR_3.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ClassifyR.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ClassifyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClassifyR’ version ‘3.6.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ClassifyR’ can be installed ... OK * used C++ compiler: ‘g++ (GCC) 10.3.1’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggupset’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .addUserLevels: no visible binding for global variable ‘median’ .dmvnorm_diag: no visible global function definition for ‘dnorm’ .doSelection : : : no visible global function definition for ‘setNames’ .doSelection : : : no visible global function definition for ‘na.omit’ .doSelection : : : no visible global function definition for ‘median’ .doSelection : : no visible binding for global variable ‘trainParams’ .doSelection : : no visible binding for global variable ‘predictParams’ .doSelection : : no visible binding for global variable ‘measurementsSubset’ .doSelection : : no visible global function definition for ‘median’ .doSelection : : no visible binding for global variable ‘aResult’ .doSelection: no visible binding for global variable ‘featuresLists’ .doTrain : : no visible global function definition for ‘median’ .filterCharacteristics: no visible global function definition for ‘na.omit’ .getEdgeLabel: no visible binding for '<<-' assignment to ‘nSamples’ .getEdgeLabel: no visible binding for global variable ‘samplesTiers’ .getEdgeLabel: no visible binding for global variable ‘nSamples’ .getFeaturesStrings : : no visible global function definition for ‘first’ .getFeaturesStrings : : no visible global function definition for ‘second’ .getFillColour: no visible binding for global variable ‘nodeColours’ .posterior_probs : : no visible global function definition for ‘dmvnorm’ .precisionPathwaysPredict: no visible binding for global variable ‘useFeatures’ .precisionPathwaysTrain: no visible global function definition for ‘setNames’ .samplesSplits : : no visible binding for global variable ‘classes’ DLDApredictInterface: no visible global function definition for ‘predict’ DMDranking : : no visible global function definition for ‘dist’ GLMpredictInterface: no visible global function definition for ‘predict’ GLMtrainInterface: no visible global function definition for ‘glm’ GLMtrainInterface: no visible binding for global variable ‘quasibinomial’ SVMpredictInterface: no visible global function definition for ‘predict’ bubblePlot.PrecisionPathways: no visible binding for global variable ‘accuracy’ bubblePlot.PrecisionPathways: no visible binding for global variable ‘cost’ bubblePlot.PrecisionPathways: no visible binding for global variable ‘Sequence’ classifyInterface: no visible binding for global variable ‘trainingMatrix’ classifyInterface: no visible binding for global variable ‘testingMatrix’ colCoxTests: no visible global function definition for ‘pnorm’ colCoxTests : : no visible global function definition for ‘coxph’ coxnetPredictInterface: no visible global function definition for ‘predict’ coxnetTrainInterface: no visible global function definition for ‘predict’ coxphPredictInterface: no visible global function definition for ‘predict’ crissCrossPlot: no visible binding for global variable ‘params’ crissCrossPlot: no visible binding for global variable ‘real’ crissCrossPlot: no visible binding for global variable ‘Var1’ crissCrossPlot: no visible binding for global variable ‘Var2’ crissCrossPlot: no visible binding for global variable ‘value’ crissCrossPlot: no visible binding for global variable ‘random’ crissCrossValidate : : : no visible global function definition for ‘predict’ crissCrossValidate : : : no visible global function definition for ‘na.omit’ differentMeansRanking : : no visible global function definition for ‘chisq.test’ edgeRranking: no visible global function definition for ‘model.matrix’ elasticNetGLMpredictInterface: no visible global function definition for ‘predict’ elasticNetGLMtrainInterface : : no visible global function definition for ‘predict’ extremeGradientBoostingPredictInterface: no visible global function definition for ‘predict’ fastCox: no visible global function definition for ‘pnorm’ fisherDiscriminant: no visible binding for global variable ‘trainingMatrix’ fisherDiscriminant: no visible binding for global variable ‘var’ flowchart.PrecisionPathways: no visible binding for global variable ‘Node’ flowchart.PrecisionPathways: no visible binding for global variable ‘Predicted’ flowchart.PrecisionPathways: no visible binding for global variable ‘Tier’ flowchart.PrecisionPathways: no visible global function definition for ‘SetGraphStyle’ flowchart.PrecisionPathways: no visible global function definition for ‘SetEdgeStyle’ flowchart.PrecisionPathways: no visible global function definition for ‘SetNodeStyle’ getLocationsAndScales: no visible global function definition for ‘setNames’ getLocationsAndScales: no visible binding for global variable ‘median’ getLocationsAndScales: no visible binding for global variable ‘sd’ getLocationsAndScales: no visible binding for global variable ‘mad’ kNNinterface: no visible global function definition for ‘setNames’ kTSPclassifier : : no visible binding for global variable ‘trainingMatrix’ kTSPclassifier : : no visible global function definition for ‘Pairs’ kTSPclassifier: no visible binding for global variable ‘testingMatrix’ likelihoodRatioRanking : : no visible global function definition for ‘dnorm’ likelihoodRatioRanking : : : no visible global function definition for ‘dnorm’ limmaRanking: no visible global function definition for ‘model.matrix’ mixModelsPredict : : no visible global function definition for ‘setNames’ mixModelsPredict : : : : no visible global function definition for ‘dnorm’ mixModelsPredict : : : no visible global function definition for ‘splinefun’ mixModelsTrain: no visible global function definition for ‘setNames’ naiveBayesKernel: no visible binding for global variable ‘density’ naiveBayesKernel : : : no visible global function definition for ‘splinefun’ naiveBayesKernel: no visible binding for global variable ‘test’ naiveBayesKernel : : no visible global function definition for ‘setNames’ pcaPredictInterface : : no visible global function definition for ‘predict’ pcaTrainInterface : : no visible global function definition for ‘prcomp’ performanceTable : : : no visible global function definition for ‘median’ performanceTable : : no visible binding for global variable ‘characteristic’ performanceTable : : no visible binding for global variable ‘value’ randomForestPredictInterface: no visible global function definition for ‘predict’ rfsrcPredictInterface: no visible global function definition for ‘predict’ strataPlot.PrecisionPathways: no visible binding for global variable ‘Tier’ strataPlot.PrecisionPathways: no visible binding for global variable ‘trueClass’ strataPlot.PrecisionPathways: no visible binding for global variable ‘Accuracy’ strataPlot.PrecisionPathways: no visible binding for global variable ‘ID’ subtractFromLocation: no visible binding for global variable ‘median’ train.DataFrame : : : : no visible global function definition for ‘na.omit’ train.DataFrame: no visible binding for global variable ‘crossValParams’ ROCplot,list : : : : no visible global function definition for ‘quantile’ 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’ crossValidate,DataFrame: no visible global function definition for ‘runif’ 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 ‘aggregate’ distribution,ClassifyResult: no visible global function definition for ‘mcols<-’ featureSetSummary,DataFrame: no visible binding for global variable ‘median’ featureSetSummary,MultiAssayExperiment: no visible binding for global variable ‘median’ featureSetSummary,matrix: no visible binding for global variable ‘median’ 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’ precisionPathwaysTrain,MultiAssayExperimentOrList: no visible global function definition for ‘setNames’ prepareData,DataFrame: no visible global function definition for ‘unqiue’ prepareData,DataFrame : : no visible binding for global variable ‘var’ 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 ‘na.omit’ runTest,DataFrame : : no visible global function definition for ‘na.omit’ runTest,MultiAssayExperiment: no visible binding for global variable ‘extrasInputs’ runTest,MultiAssayExperiment: no visible binding for global variable ‘prepArgs’ 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 ‘median’ 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’ show,PredictParams: no visible global function definition for ‘na.omit’ show,SelectParams: no visible global function definition for ‘na.omit’ show,TrainParams: no visible global function definition for ‘na.omit’ show,TransformParams: no visible global function definition for ‘na.omit’ Undefined global functions or variables: Accuracy Class FPR Freq Group ID Metric Node Pairs Predicted Sequence SetEdgeStyle SetGraphStyle SetNodeStyle TPR Tier Var1 Var2 aResult accuracy aggregate characteristic chisq.test classes colourVariable cost coxph crossValParams density dist dmvnorm dnorm extrasInputs feature featuresLists first glm key legends grouping lower mad mcols<- measurement measurements measurementsSubset median model.matrix nSamples na.omit name nodeColours overlap params pnorm prcomp predict predictParams prepArgs quantile quasibinomial random real runif samplesTiers sd second setNames size splinefun test testingMatrix top trainParams trainingMatrix trueClass type unqiue upper useFeatures value var Consider adding importFrom("base", "grouping") importFrom("stats", "aggregate", "chisq.test", "density", "dist", "dnorm", "glm", "mad", "median", "model.matrix", "na.omit", "pnorm", "prcomp", "predict", "quantile", "quasibinomial", "runif", "sd", "setNames", "splinefun", "var") 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 ... WARNING Codoc mismatches from documentation object 'samplesMetricMap': \S4method{samplesMetricMap}{list} Code: function(results, comparison = "auto", metric = "auto", featureValues = NULL, featureName = NULL, metricColours = list(c("#FFFFFF", "#CFD1F2", "#9FA3E5", "#6F75D8", "#3F48CC"), c("#FFFFFF", "#E1BFC4", "#C37F8A", "#A53F4F", "#880015")), classColours = c("#3F48CC", "#880015"), groupColours = c("darkgreen", "yellow2"), fontSizes = c(24, 16, 12, 12, 12), mapHeight = 4, title = "auto", showLegends = TRUE, xAxisLabel = "Sample Name", showXtickLabels = TRUE, yAxisLabel = "Analysis", showYtickLabels = TRUE, legendSize = grid::unit(1, "lines")) Docs: function(results, comparison = "auto", metric = "auto", featureValues = NULL, featureName = NULL, metricColours = list(c("#FFFFFF", "#CFD1F2", "#9FA3E5", "#6F75D8", "#3F48CC"), c("#FFFFFF", "#E1BFC4", "#C37F8A", "#A53F4F", "#880015")), classColours = c("#3F48CC", "#880015"), groupColours = c("darkgreen", "yellow2"), fontSizes = c(24, 16, 12, 12, 12), mapHeight = 4, title = "auto", showLegends = TRUE, xAxisLabel = "Sample Name", showXtickLabels = TRUE, yAxisLabel = "Analysis", showYtickLabels = TRUE, legendSize = grid::unit(1, "lines"), plot = TRUE) Argument names in docs not in code: plot * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'samplesMetricMap' ‘plot’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... NOTE Files named as vignettes but with no recognized vignette engine: ‘vignettes/survival.Rmd’ (Is a VignetteBuilder field missing?) * checking examples ... ERROR Running examples in ‘ClassifyR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: crossValidate > ### Title: Cross-validation to evaluate classification performance. > ### Aliases: crossValidate crossValidate,matrix-method > ### crossValidate,DataFrame-method > ### crossValidate,MultiAssayExperiment-method, > ### crossValidate,data.frame-method > ### crossValidate,MultiAssayExperimentOrList-method train.matrix > ### train.data.frame train.DataFrame train.list > ### train.MultiAssayExperiment predict.trainedByClassifyR > > ### ** Examples > > > data(asthma) > > # Compare randomForest and SVM classifiers. > result <- crossValidate(measurements, classes, classifier = c("randomForest", "SVM")) * 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: 1 ERROR, 2 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/ClassifyR.Rcheck/00check.log’ for details.