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: 2017-10-17 22:02:21 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 22:04:53 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 152.2 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 3.4.2 (2017-09-28)
* 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
runTest                  10.888  0.132  11.031
edgeRselection           10.684  0.160  11.211
ClassifyResult-class      9.480  0.192  12.845
runTests                  9.316  0.088  12.992
distribution              8.420  0.072  10.390
likelihoodRatioSelection  6.188  0.004   6.196
DMDselection              5.900  0.032   5.941
previousSelection         0.136  0.052   5.421
* 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	9.480	0.192	12.845
DMDselection	5.900	0.032	5.941
KolmogorovSmirnovSelection	4.660	0.024	4.688
KullbackLeiblerSelection	4.852	0.004	4.857
PredictParams-class	0.004	0.000	0.003
ROCplot	2.436	0.008	2.448
ResubstituteParams-class	0.000	0.000	0.001
SelectParams-class	0.008	0.000	0.010
SelectResult-class	0.004	0.000	0.001
TrainParams-class	0.004	0.000	0.007
TransformParams-class	0.000	0.000	0.001
bartlettSelection	0.720	0.000	0.718
calcPerformance	0.02	0.00	0.02
classifyInterface	0.624	0.008	0.744
distribution	8.420	0.072	10.390
edgeRselection	10.684	0.160	11.211
fisherDiscriminant	0.040	0.000	0.043
functionOrList-class	0.008	0.000	0.007
getLocationsAndScales	0.044	0.000	0.045
leveneSelection	1.960	0.000	2.965
likelihoodRatioSelection	6.188	0.004	6.196
limmaSelection	0.588	0.004	0.591
medianDifferenceSelection	0.396	0.000	0.398
mixmodels	2.496	0.008	2.563
naiveBayesKernel	0.340	0.004	0.347
nearestShrunkenCentroidPredictInterface	0.212	0.000	0.301
nearestShrunkenCentroidSelectionInterface	0.296	0.004	0.302
nearestShrunkenCentroidTrainInterface	0.1	0.0	0.1
pamrtrained-class	0.072	0.000	0.072
performancePlot	1.152	0.000	1.152
plotFeatureClasses	2.524	0.000	2.528
previousSelection	0.136	0.052	5.421
rankingPlot	1.628	0.108	4.003
runTest	10.888	0.132	11.031
runTests	9.316	0.088	12.992
samplesMetricMap	0.980	0.032	1.016
selectionPlot	2.300	0.064	4.707
subtractFromLocation	0.044	0.004	0.046