############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClassifyR_3.2.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/ClassifyR.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-apple-darwin17.0 (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 ‘3.2.7’ * 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 ... WARNING Found the following significant warnings: coxformatrices.cpp:526:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:527:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:567:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:568:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:654:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:655:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] See ‘/Users/biocbuild/bbs-3.16-bioc/meat/ClassifyR.Rcheck/00install.out’ for details. * 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 ... NOTE Package in Depends field not imported from: ‘BiocParallel’ 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 .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’ .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’ CrossValParams: no visible global function definition for ‘bpparam’ 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 ‘binomial’ SVMpredictInterface: no visible global function definition for ‘predict’ 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’ 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’ generateCrossValParams: no visible global function definition for ‘SerialParam’ 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 ‘SerialParam’ pcaTrainInterface : : no visible global function definition for ‘prcomp’ prevalTrainInterface: no visible global function definition for ‘SerialParam’ prevalTrainInterface: no visible global function definition for ‘bpmapply’ randomForestPredictInterface: no visible global function definition for ‘predict’ rfsrcPredictInterface: no visible global function definition for ‘predict’ 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 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 ‘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’ prepareData,DataFrame: no visible binding for global variable ‘var’ rankingPlot,list: no visible global function definition for ‘bpparam’ rankingPlot,list: no visible global function definition for ‘bpmapply’ rankingPlot,list: no visible global function definition for ‘bplapply’ 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’ runTests,DataFrame: no visible global function definition for ‘bpmapply’ 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 ‘bpparam’ selectionPlot,list: no visible global function definition for ‘bpmapply’ selectionPlot,list: no visible global function definition for ‘bplapply’ 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: ..density.. Class FPR Freq Group ID Metric Pairs SerialParam TPR aResult aggregate allPredictions binomial bplapply bpmapply bpparam chisq.test classes colourVariable coxph crossValParams density dist dmvnorm dnorm extrasInputs feature featuresLists first glm key legends grouping lower mad mcols<- measurement measurements measurementsSubset median model.matrix na.omit name overlap pnorm prcomp predict predictParams prepArgs quantile runif sd second setNames size splinefun test testingMatrix top trainParams trainingMatrix type upper value var Consider adding importFrom("base", "grouping") importFrom("stats", "aggregate", "binomial", "chisq.test", "density", "dist", "dnorm", "glm", "mad", "median", "model.matrix", "na.omit", "pnorm", "prcomp", "predict", "quantile", "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 ... 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 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’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed crossValidate 994.669 107.206 565.463 ClassifyResult-class 228.854 28.751 120.069 distribution 225.094 29.303 107.563 runTests 8.232 2.195 4.467 * 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 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.16-bioc/meat/ClassifyR.Rcheck/00check.log’ for details.