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### Running command:
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###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClassifyR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings ClassifyR_3.2.7.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/ClassifyR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 whether package 'ClassifyR' can be installed ... OK
* 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 : <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'
.getFeaturesStrings : <anonymous>: no visible global function
  definition for 'first'
.getFeaturesStrings : <anonymous>: no visible global function
  definition for 'second'
.posterior_probs : <anonymous>: no visible global function definition
  for 'dmvnorm'
.samplesSplits : <anonymous>: no visible binding for global variable
  'classes'
CrossValParams: no visible global function definition for 'bpparam'
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 '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 : <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'
differentMeansRanking : <anonymous>: 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 : <anonymous>: 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 : <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: no visible global function definition for
  'SerialParam'
pcaTrainInterface : <anonymous>: 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 : <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'
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 : <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'
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 : <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'
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 : <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:
  ..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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/ClassifyR/libs/x64/ClassifyR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
crossValidate        1192.59 130.79  772.41
distribution          282.42  34.55  161.76
ClassifyResult-class  274.91  33.42  156.18
runTests                3.31   0.09   38.60
selectionPlot           1.80   0.07   12.31
rankingPlot             1.10   0.06   12.00
* 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: 4 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.