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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClassifyR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ClassifyR_2.15.1.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ClassifyR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ClassifyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ClassifyR' version '2.15.1'
* 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 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getFeaturesStrings : <anonymous>: no visible global function
  definition for 'first'
.getFeaturesStrings : <anonymous>: no visible global function
  definition for 'second'
.getFeaturesStrings : <anonymous> : <anonymous>: no visible global
  function definition for 'first'
.getFeaturesStrings : <anonymous> : <anonymous>: no visible global
  function definition for 'second'
.posterior_probs : <anonymous>: no visible global function definition
  for 'dmvnorm'
ROCplot,list : <anonymous>: no visible binding for global variable
  'FPR'
ROCplot,list : <anonymous>: no visible binding for global variable
  'TPR'
easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no
  visible binding for global variable 'measurements'
easyHardClassifierTrain,MultiAssayExperiment: no visible binding for
  global variable 'datasetName'
easyHardClassifierTrain,MultiAssayExperiment: no visible binding for
  global variable 'classificationName'
kTSPclassifier,DataFrame : <anonymous>: no visible global function
  definition for 'Pairs'
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'
rankingPlot,list: no visible binding for global variable 'top'
rankingPlot,list: no visible binding for global variable 'overlap'
runTest,DataFrame: no visible binding for global variable 'setsNodes'
runTestEasyHard,MultiAssayExperiment: no visible binding for global
  variable 'setsNodes'
runTests,DataFrame: no visible global function definition for 'mcols'
runTests,DataFrame: no visible binding for global variable 'setsNodes'
runTests,DataFrame: no visible binding for global variable 'dataset'
runTests,DataFrame : <anonymous>: no visible global function definition
  for 'mcols'
runTests,DataFrame : <anonymous>: no visible global function definition
  for 'mcols<-'
runTests,DataFrame: no visible global function definition for 'mcols<-'
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
  variable 'setsNodes'
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
  variable '.iteration'
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 'size'
selectionPlot,list: no visible binding for global variable 'Freq'
Undefined global functions or variables:
  ..density.. .iteration Class FPR Freq Group ID Metric Pairs TPR
  classificationName dataset datasetName dmvnorm first key legends
  grouping mcols mcols<- measurement measurements name overlap second
  setsNodes size top type value
Consider adding
  importFrom("base", "grouping")
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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
DMDselection           4.92   0.17    5.09
runTests               2.15   0.22   40.64
distribution           1.73   0.17   26.56
selectionPlot          1.82   0.03    7.75
ClassifyResult-class   1.53   0.20   43.23
previousSelection      1.61   0.03   22.07
previousTrained        1.54   0.05   20.15
rankingPlot            1.15   0.02    8.08
elasticNetGLMinterface 0.87   0.03   17.56
elasticNetFeatures     0.81   0.05   16.52
* 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 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.