BioC 3.5: CHECK report for ClassifyR on malbec2

Package: ClassifyR

Version: 1.10.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.10.2.tar.gz

StartedAt: 2017-08-15 21:57:56 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:00:23 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 146.5 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.10.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ClassifyR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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
ClassifyResult-class     10.444  0.268  13.321
edgeRselection           10.480  0.216  10.726
runTest                   9.440  0.080   9.525
distribution              8.924  0.184  11.112
runTests                  7.288  0.068  10.276
likelihoodRatioSelection  6.024  0.004   6.033
DMDselection              5.832  0.064   5.901
KullbackLeiblerSelection  5.720  0.000   5.729
previousSelection         0.148  0.056   5.498
* 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
  ‘/home/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	10.444	0.268	13.321
DMDselection	5.832	0.064	5.901
KolmogorovSmirnovSelection	4.800	0.004	4.806
KullbackLeiblerSelection	5.720	0.000	5.729
PredictParams-class	0.000	0.000	0.003
ROCplot	2.016	0.000	2.017
ResubstituteParams-class	0.000	0.000	0.001
SelectParams-class	0.012	0.000	0.009
SelectResult-class	0.000	0.000	0.001
TrainParams-class	0.008	0.000	0.006
TransformParams-class	0.000	0.000	0.001
bartlettSelection	0.656	0.000	0.657
calcPerformance	0.004	0.000	0.005
classifyInterface	0.684	0.004	0.705
distribution	8.924	0.184	11.112
edgeRselection	10.480	0.216	10.726
fisherDiscriminant	0.028	0.000	0.029
functionOrList-class	0.000	0.004	0.005
getLocationsAndScales	0.016	0.008	0.024
leveneSelection	1.668	0.008	2.467
likelihoodRatioSelection	6.024	0.004	6.033
limmaSelection	0.668	0.000	0.668
medianDifferenceSelection	0.416	0.004	0.422
mixmodels	3.060	0.000	3.122
naiveBayesKernel	0.356	0.000	0.355
nearestShrunkenCentroidPredictInterface	0.168	0.004	0.197
nearestShrunkenCentroidSelectionInterface	0.344	0.004	0.347
nearestShrunkenCentroidTrainInterface	0.072	0.000	0.072
pamrtrained-class	0.040	0.000	0.042
performancePlot	1.528	0.000	1.528
plotFeatureClasses	3.276	0.000	3.280
previousSelection	0.148	0.056	5.498
rankingPlot	1.896	0.096	4.366
runTest	9.440	0.080	9.525
runTests	7.288	0.068	10.276
samplesMetricMap	0.744	0.040	0.783
selectionPlot	1.684	0.080	3.832
subtractFromLocation	0.048	0.000	0.047