Package: ClassifyR

Version: 1.12.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.12.2.tar.gz

StartedAt: 2018-04-12 01:45:29 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:48:17 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 168.6 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_1.12.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ClassifyR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.2’
* 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 ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
* 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             10.896  0.298  11.492
runTest                    10.067  0.268  10.547
distribution                9.734  0.310  12.832
ClassifyResult-class        9.641  0.254  12.584
runTests                    8.506  0.157  10.839
DMDselection                7.567  0.151   7.846
likelihoodRatioSelection    7.445  0.117   7.722
KolmogorovSmirnovSelection  6.494  0.061   6.714
KullbackLeiblerSelection    6.191  0.067   6.369
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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	9.641	0.254	12.584
DMDselection	7.567	0.151	7.846
KolmogorovSmirnovSelection	6.494	0.061	6.714
KullbackLeiblerSelection	6.191	0.067	6.369
PredictParams-class	0.003	0.000	0.004
ROCplot	2.470	0.005	2.531
ResubstituteParams-class	0.002	0.000	0.003
SelectParams-class	0.012	0.001	0.012
SelectResult-class	0.001	0.000	0.002
TrainParams-class	0.009	0.001	0.009
TransformParams-class	0.001	0.000	0.001
bartlettSelection	0.794	0.004	0.811
calcPerformance	0.023	0.000	0.023
classifyInterface	0.524	0.085	0.614
distribution	9.734	0.310	12.832
edgeRselection	10.896	0.298	11.492
fisherDiscriminant	0.034	0.000	0.036
functionOrList-class	0.007	0.001	0.010
getLocationsAndScales	0.028	0.001	0.029
leveneSelection	1.321	0.013	1.357
likelihoodRatioSelection	7.445	0.117	7.722
limmaSelection	0.790	0.010	0.818
medianDifferenceSelection	0.565	0.005	0.587
mixmodels	3.512	0.037	3.636
naiveBayesKernel	0.451	0.013	0.474
nearestShrunkenCentroidPredictInterface	0.188	0.005	0.202
nearestShrunkenCentroidSelectionInterface	0.314	0.006	0.327
nearestShrunkenCentroidTrainInterface	0.092	0.004	0.097
pamrtrained-class	0.064	0.002	0.065
performancePlot	1.532	0.020	1.578
plotFeatureClasses	3.168	0.009	3.259
previousSelection	0.159	0.088	2.050
rankingPlot	1.745	0.157	1.985
runTest	10.067	0.268	10.547
runTests	8.506	0.157	10.839
samplesMetricMap	1.076	0.136	1.265
selectionPlot	2.051	0.138	2.297
subtractFromLocation	0.084	0.001	0.089