BioC 3.5: CHECK report for ClassifyR on tokay2

Package: ClassifyR

Version: 1.10.2

Command: rm -rf ClassifyR.buildbin-libdir ClassifyR.Rcheck && mkdir ClassifyR.buildbin-libdir ClassifyR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ClassifyR.buildbin-libdir ClassifyR_1.10.2.tar.gz >ClassifyR.Rcheck\00install.out 2>&1 && cp ClassifyR.Rcheck\00install.out ClassifyR-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ClassifyR.buildbin-libdir --install="check:ClassifyR-install.out" --force-multiarch --no-vignettes --timings ClassifyR_1.10.2.tar.gz

StartedAt: 2017-08-15 22:43:52 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:49:42 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 350.5 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf ClassifyR.buildbin-libdir ClassifyR.Rcheck && mkdir ClassifyR.buildbin-libdir ClassifyR.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ClassifyR.buildbin-libdir ClassifyR_1.10.2.tar.gz >ClassifyR.Rcheck\00install.out 2>&1 && cp ClassifyR.Rcheck\00install.out ClassifyR-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ClassifyR.buildbin-libdir --install="check:ClassifyR-install.out" --force-multiarch --no-vignettes --timings ClassifyR_1.10.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ClassifyR.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.10.2'
* 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
* loading checks for arch 'i386'
** 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 loading without being on the library search path ... OK
* loading checks for arch 'x64'
** 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 loading without being on the library search path ... 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
.doTest : <anonymous>: no visible global function definition for
  'capture.output'
KolmogorovSmirnovSelection,ExpressionSet : <anonymous>: no visible
  global function definition for 'ks.test'
PredictParams,ANY: no visible binding for global variable 'predict'
TrainParams,ANY: no visible binding for global variable 'dlda'
bartlettSelection,ExpressionSet : <anonymous>: no visible global
  function definition for 'bartlett.test'
edgeRselection,ExpressionSet: no visible global function definition for
  'model.matrix'
fisherDiscriminant,ExpressionSet: no visible binding for global
  variable 'var'
getLocationsAndScales,ExpressionSet: no visible binding for global
  variable 'median'
getLocationsAndScales,ExpressionSet: no visible binding for global
  variable 'sd'
getLocationsAndScales,ExpressionSet: no visible binding for global
  variable 'mad'
likelihoodRatioSelection,ExpressionSet : <anonymous>: no visible global
  function definition for 'dnorm'
limmaSelection,ExpressionSet: no visible global function definition for
  'model.matrix'
medianDifferenceSelection,ExpressionSet: no visible binding for global
  variable 'median'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
  <anonymous>: no visible global function definition for 'dnorm'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous>: no
  visible binding for global variable 'classes'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  'largerClass'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  'classes'
naiveBayesKernel,ExpressionSet: no visible binding for global variable
  'density'
naiveBayesKernel,ExpressionSet: no visible binding for global variable
  'featureValues'
naiveBayesKernel,ExpressionSet : <anonymous>: no visible global
  function definition for 'splinefun'
performancePlot,list: no visible global function definition for
  'reformulate'
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
  global variable 'expr'
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
  global variable '..density..'
previousSelection,ExpressionSet: no visible global function definition
  for 'na.omit'
rankingPlot,list: no visible global function definition for
  'reformulate'
runTests,ExpressionSet: no visible global function definition for
  'combn'
samplesMetricMap,list: no visible binding for global variable 'Class'
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'
selectionPlot,list: no visible binding for global variable 'Freq'
selectionPlot,list: no visible global function definition for
  'reformulate'
subtractFromLocation,ExpressionSet: no visible binding for global
  variable 'median'
Undefined global functions or variables:
  ..density.. Class Freq Metric bartlett.test capture.output classes
  combn density dlda dnorm expr featureValues ks.test largerClass mad
  median model.matrix na.omit name predict reformulate sd splinefun
  type var
Consider adding
  importFrom("stats", "bartlett.test", "density", "dnorm", "ks.test",
             "mad", "median", "model.matrix", "na.omit", "predict",
             "reformulate", "sd", "splinefun", "var")
  importFrom("utils", "capture.output", "combn")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
ClassifyResult-class       13.03   0.52   25.41
edgeRselection             10.58   0.30   11.28
runTest                     9.72   0.25    9.97
distribution                8.37   0.34   14.50
runTests                    7.00   0.17   13.02
DMDselection                6.93   0.03    6.97
KolmogorovSmirnovSelection  5.61   0.00    5.61
likelihoodRatioSelection    5.50   0.11    5.61
KullbackLeiblerSelection    5.42   0.00    5.42
previousSelection           0.11   0.06   10.09
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
edgeRselection             14.31   0.17   14.48
distribution               12.96   0.35   20.45
runTest                    11.16   0.20   11.36
runTests                    8.61   0.25   15.65
likelihoodRatioSelection    7.49   0.00    7.49
ClassifyResult-class        7.06   0.36   13.99
DMDselection                6.21   0.02    6.22
KullbackLeiblerSelection    5.67   0.00    5.68
KolmogorovSmirnovSelection  5.52   0.00    5.51
selectionPlot               2.72   0.02    5.27
previousSelection           0.12   0.00   11.13
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'ClassifyR' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'performance' in package 'ClassifyR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'ClassifyR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ClassifyR' as ClassifyR_1.10.2.zip
* DONE (ClassifyR)

name	user	system	elapsed
ClassifyResult-class	13.03	0.52	25.41
DMDselection	6.93	0.03	6.97
KolmogorovSmirnovSelection	5.61	0.00	5.61
KullbackLeiblerSelection	5.42	0.00	5.42
PredictParams-class	0	0	0
ROCplot	1.97	0.00	2.02
ResubstituteParams-class	0	0	0
SelectParams-class	0.02	0.00	0.01
SelectResult-class	0	0	0
TrainParams-class	0.01	0.00	0.02
TransformParams-class	0	0	0
bartlettSelection	0.63	0.00	0.62
calcPerformance	0.01	0.00	0.02
classifyInterface	0.69	0.11	0.81
distribution	8.37	0.34	14.50
edgeRselection	10.58	0.30	11.28
fisherDiscriminant	0.01	0.00	0.01
functionOrList-class	0	0	0
getLocationsAndScales	0.04	0.00	0.03
leveneSelection	1.20	0.03	1.24
likelihoodRatioSelection	5.50	0.11	5.61
limmaSelection	0.54	0.00	0.53
medianDifferenceSelection	0.37	0.00	0.38
mixmodels	3.03	0.00	3.28
naiveBayesKernel	0.45	0.00	0.45
nearestShrunkenCentroidPredictInterface	0.22	0.02	0.23
nearestShrunkenCentroidSelectionInterface	0.39	0.01	0.41
nearestShrunkenCentroidTrainInterface	0.11	0.02	0.13
pamrtrained-class	0.07	0.00	0.06
performancePlot	1.22	0.00	1.22
plotFeatureClasses	2.40	0.00	2.41
previousSelection	0.11	0.06	10.09
rankingPlot	1.52	0.00	4.11
runTest	9.72	0.25	9.97
runTests	7.00	0.17	13.02
samplesMetricMap	0.81	0.00	0.81
selectionPlot	1.71	0.03	3.97
subtractFromLocation	0.04	0.00	0.05

name	user	system	elapsed
ClassifyResult-class	7.06	0.36	13.99
DMDselection	6.21	0.02	6.22
KolmogorovSmirnovSelection	5.52	0.00	5.51
KullbackLeiblerSelection	5.67	0.00	5.68
PredictParams-class	0	0	0
ROCplot	2.37	0.00	2.37
ResubstituteParams-class	0.02	0.00	0.02
SelectParams-class	0.01	0.00	0.01
SelectResult-class	0	0	0
TrainParams-class	0.02	0.00	0.02
TransformParams-class	0	0	0
bartlettSelection	0.87	0.00	0.88
calcPerformance	0	0	0
classifyInterface	1.14	0.04	1.19
distribution	12.96	0.35	20.45
edgeRselection	14.31	0.17	14.48
fisherDiscriminant	0.11	0.00	0.11
functionOrList-class	0	0	0
getLocationsAndScales	0.03	0.00	0.03
leveneSelection	1.84	0.01	1.86
likelihoodRatioSelection	7.49	0.00	7.49
limmaSelection	0.66	0.00	0.66
medianDifferenceSelection	0.47	0.02	0.48
mixmodels	3.26	0.00	3.33
naiveBayesKernel	0.47	0.00	0.47
nearestShrunkenCentroidPredictInterface	0.25	0.01	0.33
nearestShrunkenCentroidSelectionInterface	0.44	0.00	0.43
nearestShrunkenCentroidTrainInterface	0.10	0.00	0.11
pamrtrained-class	0.07	0.00	0.06
performancePlot	1.34	0.00	1.35
plotFeatureClasses	2.77	0.00	2.76
previousSelection	0.12	0.00	11.13
rankingPlot	1.81	0.02	4.54
runTest	11.16	0.20	11.36
runTests	8.61	0.25	15.65
samplesMetricMap	0.96	0.00	0.97
selectionPlot	2.72	0.02	5.27
subtractFromLocation	0.10	0.00	0.09