BioC 3.5: CHECK report for ClassifyR on toluca2

Package: ClassifyR

Version: 1.9.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.9.3.tar.gz

StartedAt: 2017-04-23 01:50:19 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 01:53:48 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 208.7 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_1.9.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.9.3’
* 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             12.824  0.352  13.356
distribution               10.032  0.249  14.734
runTest                     9.898  0.179  12.990
ClassifyResult-class        9.429  0.212  15.369
runTests                    9.024  0.237  16.576
DMDselection                8.943  0.188   9.207
likelihoodRatioSelection    8.992  0.121   9.254
KullbackLeiblerSelection    7.758  0.095   7.916
KolmogorovSmirnovSelection  7.715  0.099   7.895
selectionPlot               2.303  0.158   5.017
rankingPlot                 2.148  0.165   6.302
previousSelection           0.169  0.105  10.985
* 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	9.429	0.212	15.369
DMDselection	8.943	0.188	9.207
KolmogorovSmirnovSelection	7.715	0.099	7.895
KullbackLeiblerSelection	7.758	0.095	7.916
PredictParams-class	0.003	0.000	0.003
ROCplot	3.093	0.007	3.120
ResubstituteParams-class	0.002	0.000	0.002
SelectParams-class	0.013	0.001	0.013
SelectResult-class	0.002	0.000	0.001
TrainParams-class	0.008	0.000	0.009
TransformParams-class	0.001	0.000	0.002
bartlettSelection	1.005	0.003	1.010
calcPerformance	0.007	0.000	0.008
classifyInterface	0.608	0.050	0.670
distribution	10.032	0.249	14.734
edgeRselection	12.824	0.352	13.356
fisherDiscriminant	0.048	0.000	0.052
functionOrList-class	0.008	0.001	0.009
getLocationsAndScales	0.041	0.002	0.042
leveneSelection	2.320	0.022	2.397
likelihoodRatioSelection	8.992	0.121	9.254
limmaSelection	1.394	0.014	1.448
medianDifferenceSelection	0.633	0.003	0.649
mixmodels	4.152	0.021	4.245
naiveBayesKernel	0.488	0.027	0.535
nearestShrunkenCentroidPredictInterface	0.238	0.006	0.247
nearestShrunkenCentroidSelectionInterface	0.504	0.037	0.542
nearestShrunkenCentroidTrainInterface	0.118	0.002	0.121
pamrtrained-class	0.066	0.003	0.068
performancePlot	1.786	0.011	1.831
plotFeatureClasses	3.966	0.012	4.007
previousSelection	0.169	0.105	10.985
rankingPlot	2.148	0.165	6.302
runTest	9.898	0.179	12.990
runTests	9.024	0.237	16.576
samplesMetricMap	1.089	0.127	1.223
selectionPlot	2.303	0.158	5.017
subtractFromLocation	0.076	0.001	0.078