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: 2017-10-18 01:45:07 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:48:08 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 180.8 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 3.4.2 (2017-09-28)
* 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             11.705  0.358  12.490
runTest                    10.794  0.276  13.722
distribution               10.059  0.331  13.063
ClassifyResult-class        9.707  0.274  12.858
runTests                    8.622  0.173  13.558
DMDselection                7.625  0.176   8.152
likelihoodRatioSelection    7.512  0.116   7.869
KolmogorovSmirnovSelection  6.347  0.083   6.622
KullbackLeiblerSelection    6.233  0.055   6.478
rankingPlot                 1.998  0.212   6.370
previousSelection           0.187  0.125   9.135
* 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	9.707	0.274	12.858
DMDselection	7.625	0.176	8.152
KolmogorovSmirnovSelection	6.347	0.083	6.622
KullbackLeiblerSelection	6.233	0.055	6.478
PredictParams-class	0.002	0.000	0.002
ROCplot	2.445	0.018	2.528
ResubstituteParams-class	0.002	0.000	0.002
SelectParams-class	0.016	0.001	0.017
SelectResult-class	0.001	0.001	0.001
TrainParams-class	0.013	0.000	0.014
TransformParams-class	0.002	0.000	0.002
bartlettSelection	0.886	0.007	0.928
calcPerformance	0.027	0.000	0.028
classifyInterface	0.564	0.065	0.643
distribution	10.059	0.331	13.063
edgeRselection	11.705	0.358	12.490
fisherDiscriminant	0.041	0.000	0.044
functionOrList-class	0.007	0.001	0.008
getLocationsAndScales	0.031	0.001	0.033
leveneSelection	1.982	0.027	2.082
likelihoodRatioSelection	7.512	0.116	7.869
limmaSelection	0.820	0.006	0.864
medianDifferenceSelection	0.560	0.005	0.577
mixmodels	3.609	0.029	3.729
naiveBayesKernel	0.518	0.041	0.571
nearestShrunkenCentroidPredictInterface	0.203	0.006	0.220
nearestShrunkenCentroidSelectionInterface	0.370	0.004	0.402
nearestShrunkenCentroidTrainInterface	0.132	0.003	0.138
pamrtrained-class	0.060	0.001	0.061
performancePlot	1.550	0.012	1.606
plotFeatureClasses	3.486	0.022	4.011
previousSelection	0.187	0.125	9.135
rankingPlot	1.998	0.212	6.370
runTest	10.794	0.276	13.722
runTests	8.622	0.173	13.558
samplesMetricMap	1.027	0.121	1.171
selectionPlot	1.717	0.140	4.373
subtractFromLocation	0.065	0.001	0.070