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### Running command:
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### /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_3.6.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ClassifyR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘3.6.5’
* 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-3.18-bioc-mac-arm64/meat/ClassifyR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 : <anonymous> : <anonymous>: no visible global function
definition for ‘setNames’
.doSelection : <anonymous> : <anonymous>: no visible global function
definition for ‘na.omit’
.doSelection : <anonymous> : <anonymous>: no visible global function
definition for ‘median’
.doSelection : <anonymous>: no visible binding for global variable
‘trainParams’
.doSelection : <anonymous>: no visible binding for global variable
‘predictParams’
.doSelection : <anonymous>: no visible binding for global variable
‘measurementsSubset’
.doSelection : <anonymous>: no visible global function definition for
‘median’
.doSelection : <anonymous>: no visible binding for global variable
‘aResult’
.doSelection: no visible binding for global variable ‘featuresLists’
.doTrain : <anonymous>: 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 : <anonymous>: no visible global function
definition for ‘first’
.getFeaturesStrings : <anonymous>: no visible global function
definition for ‘second’
.getFillColour: no visible binding for global variable ‘nodeColours’
.posterior_probs : <anonymous>: no visible global function definition
for ‘dmvnorm’
.precisionPathwaysPredict: no visible binding for global variable
‘useFeatures’
.precisionPathwaysTrain: no visible global function definition for
‘setNames’
.samplesSplits : <anonymous>: no visible binding for global variable
‘classes’
DLDApredictInterface: no visible global function definition for
‘predict’
DMDranking : <anonymous>: 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 : <anonymous>: 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 : <anonymous> : <anonymous>: no visible global
function definition for ‘predict’
crissCrossValidate : <anonymous> : <anonymous>: no visible global
function definition for ‘na.omit’
differentMeansRanking : <anonymous>: 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 : <anonymous>: no visible binding for global variable
‘trainingMatrix’
kTSPclassifier : <anonymous>: no visible global function definition for
‘Pairs’
kTSPclassifier: no visible binding for global variable ‘testingMatrix’
likelihoodRatioRanking : <anonymous>: no visible global function
definition for ‘dnorm’
likelihoodRatioRanking : <anonymous> : <anonymous>: no visible global
function definition for ‘dnorm’
limmaRanking: no visible global function definition for ‘model.matrix’
mixModelsPredict : <anonymous>: no visible global function definition
for ‘setNames’
mixModelsPredict : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘dnorm’
mixModelsPredict : <anonymous> : <anonymous>: no visible global
function definition for ‘splinefun’
mixModelsTrain: no visible global function definition for ‘setNames’
naiveBayesKernel: no visible binding for global variable ‘density’
naiveBayesKernel : <anonymous> : <anonymous>: no visible global
function definition for ‘splinefun’
naiveBayesKernel: no visible binding for global variable ‘test’
naiveBayesKernel : <anonymous>: no visible global function definition
for ‘setNames’
pcaPredictInterface : <anonymous>: no visible global function
definition for ‘predict’
pcaTrainInterface : <anonymous>: no visible global function definition
for ‘prcomp’
penalisedGLMpredictInterface: no visible global function definition for
‘predict’
penalisedGLMtrainInterface : <anonymous>: no visible global function
definition for ‘predict’
performanceTable : <anonymous> : <anonymous>: no visible global
function definition for ‘median’
performanceTable : <anonymous>: no visible binding for global variable
‘characteristic’
performanceTable : <anonymous>: 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 : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘na.omit’
train.DataFrame: no visible binding for global variable
‘crossValParams’
ROCplot,list : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘quantile’
ROCplot,list : <anonymous>: no visible binding for global variable
‘FPR’
ROCplot,list : <anonymous>: no visible binding for global variable
‘TPR’
ROCplot,list : <anonymous>: no visible binding for global variable
‘lower’
ROCplot,list : <anonymous>: 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 : <anonymous>: no visible binding for
global variable ‘measurement’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable ‘density’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable ‘legends grouping’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable ‘key’
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
global variable ‘value’
plotFeatureClasses,DataFrame : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 : <anonymous>: 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 documentation object 'crossValidate':
\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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
crossValidate 1048.034 40.917 791.102
ClassifyResult-class 219.424 10.585 146.733
distribution 213.574 10.325 146.135
runTests 8.309 3.803 5.722
* 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 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/ClassifyR.Rcheck/00check.log’
for details.
