##############################################################################
##############################################################################
###
### 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_3.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/ClassifyR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClassifyR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClassifyR’ version ‘3.8.0’
* 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 ... 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-mac-arm64/meat/ClassifyR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* 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 code 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’
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’
DLDApredictInterface: no visible global function definition for
‘predict’
DMDranking : <anonymous>: no visible global function definition for
‘dist’
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’
GLMpredictInterface: no visible global function definition for
‘predict’
GLMtrainInterface: no visible global function definition for ‘glm’
GLMtrainInterface: no visible binding for global variable
‘quasibinomial’
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’
SVMpredictInterface: no visible global function definition for
‘predict’
train.DataFrame : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for ‘na.omit’
train.DataFrame: no visible binding for global variable
‘crossValParams’
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,matrix: no visible binding for global variable
‘median’
featureSetSummary,MultiAssayExperiment: 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’
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’
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 Accuracy aggregate aResult characteristic chisq.test Class
classes colourVariable cost coxph crossValParams density dist dmvnorm
dnorm extrasInputs feature featuresLists first FPR Freq glm Group ID
key legends grouping lower mad mcols<- measurement measurements
measurementsSubset median Metric model.matrix na.omit name Node
nodeColours nSamples overlap Pairs params pnorm prcomp predict
Predicted predictParams prepArgs quantile quasibinomial random real
samplesTiers sd second Sequence SetEdgeStyle SetGraphStyle setNames
SetNodeStyle size splinefun test testingMatrix Tier top TPR
trainingMatrix trainParams trueClass type unqiue upper useFeatures
value var Var1 Var2
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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
crossValidate 414.727 80.871 225.556
ClassifyResult-class 88.194 20.760 39.892
distribution 87.884 20.746 39.166
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.19-bioc-mac-arm64/meat/ClassifyR.Rcheck/00check.log’
for details.
