############################################################################## ############################################################################## ### ### 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_3.7.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ClassifyR.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ClassifyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClassifyR’ version ‘3.7.4’ * 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 ... WARNING Found the following significant warnings: coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ClassifyR.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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’ 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’ penalisedGLMpredictInterface: no visible global function definition for ‘predict’ penalisedGLMtrainInterface : : no visible global function definition for ‘predict’ 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’ 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 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", "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 Rd file 'crossValidate.Rd': \S4method{crossValidate}{MultiAssayExperimentOrList} Code: function(measurements, outcome, nFeatures = 20, selectionMethod = "auto", selectionOptimisation = "Resubstitution", performanceType = "auto", classifier = "auto", multiViewMethod = "none", assayCombinations = "all", nFolds = 5, nRepeats = 20, nCores = 1, characteristicsLabel = NULL, extraParams = NULL, verbose = 0) Docs: function(measurements, outcome, nFeatures = 20, selectionMethod = "auto", selectionOptimisation = "Resubstitution", performanceType = "auto", classifier = "auto", multiViewMethod = "none", assayCombinations = "all", nFolds = 5, nRepeats = 20, nCores = 1, characteristicsLabel = NULL, extraParams = NULL) Argument names in code not in docs: verbose \S4method{crossValidate}{data.frame} Code: function(measurements, outcome, nFeatures = 20, selectionMethod = "auto", selectionOptimisation = "Resubstitution", performanceType = "auto", classifier = "auto", multiViewMethod = "none", assayCombinations = "all", nFolds = 5, nRepeats = 20, nCores = 1, characteristicsLabel = NULL, extraParams = NULL, verbose = 0) Docs: function(measurements, outcome, nFeatures = 20, selectionMethod = "auto", selectionOptimisation = "Resubstitution", performanceType = "auto", classifier = "auto", multiViewMethod = "none", assayCombinations = "all", nFolds = 5, nRepeats = 20, nCores = 1, characteristicsLabel = NULL, extraParams = NULL) Argument names in code not in docs: verbose \S4method{crossValidate}{matrix} Code: function(measurements, outcome, nFeatures = 20, selectionMethod = "auto", selectionOptimisation = "Resubstitution", performanceType = "auto", classifier = "auto", multiViewMethod = "none", assayCombinations = "all", nFolds = 5, nRepeats = 20, nCores = 1, characteristicsLabel = NULL, extraParams = NULL, verbose = 0) Docs: function(measurements, outcome, nFeatures = 20, selectionMethod = "auto", selectionOptimisation = "Resubstitution", performanceType = "auto", classifier = "auto", multiViewMethod = "none", assayCombinations = "all", nFolds = 5, nRepeats = 20, nCores = 1, characteristicsLabel = NULL, extraParams = NULL) Argument names in code not in docs: verbose * 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 ...