BioC 3.5: CHECK report for ClassifyR on veracruz2

Package: ClassifyR

Version: 1.10.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.10.2.tar.gz

StartedAt: 2017-08-16 01:01:15 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:04:13 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 177.6 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.10.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ClassifyR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘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 for sufficient/correct file permissions ... 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 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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
edgeRselection             11.582  0.308  12.325
runTest                    10.327  0.226  11.859
ClassifyResult-class        9.466  0.236  12.446
distribution                9.275  0.231  12.075
runTests                    9.026  0.158  13.261
likelihoodRatioSelection    7.552  0.094   7.939
DMDselection                7.326  0.141   7.685
KolmogorovSmirnovSelection  6.419  0.071   6.703
KullbackLeiblerSelection    6.373  0.057   6.637
mixmodels                   3.976  0.021   5.110
rankingPlot                 1.944  0.178   6.095
previousSelection           0.154  0.088   7.407
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.

* 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
* DONE (ClassifyR)

name	user	system	elapsed
ClassifyResult-class	9.466	0.236	12.446
DMDselection	7.326	0.141	7.685
KolmogorovSmirnovSelection	6.419	0.071	6.703
KullbackLeiblerSelection	6.373	0.057	6.637
PredictParams-class	0.003	0.000	0.003
ROCplot	2.541	0.028	2.629
ResubstituteParams-class	0.002	0.000	0.002
SelectParams-class	0.011	0.001	0.012
SelectResult-class	0.001	0.000	0.001
TrainParams-class	0.007	0.000	0.007
TransformParams-class	0.001	0.000	0.002
bartlettSelection	0.800	0.002	0.821
calcPerformance	0.004	0.000	0.004
classifyInterface	0.442	0.057	0.524
distribution	9.275	0.231	12.075
edgeRselection	11.582	0.308	12.325
fisherDiscriminant	0.036	0.000	0.040
functionOrList-class	0.008	0.001	0.008
getLocationsAndScales	0.027	0.001	0.030
leveneSelection	1.976	0.021	2.102
likelihoodRatioSelection	7.552	0.094	7.939
limmaSelection	0.777	0.005	0.798
medianDifferenceSelection	0.567	0.004	0.656
mixmodels	3.976	0.021	5.110
naiveBayesKernel	0.501	0.014	0.647
nearestShrunkenCentroidPredictInterface	0.214	0.006	0.276
nearestShrunkenCentroidSelectionInterface	0.434	0.004	0.558
nearestShrunkenCentroidTrainInterface	0.109	0.003	0.142
pamrtrained-class	0.064	0.001	0.082
performancePlot	1.744	0.007	2.253
plotFeatureClasses	3.796	0.020	4.883
previousSelection	0.154	0.088	7.407
rankingPlot	1.944	0.178	6.095
runTest	10.327	0.226	11.859
runTests	9.026	0.158	13.261
samplesMetricMap	0.907	0.116	1.051
selectionPlot	1.791	0.148	4.424
subtractFromLocation	0.065	0.001	0.066