BioC 3.4: CHECK report for ClassifyR on morelia

Package: ClassifyR

Version: 1.7.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.7.4.tar.gz

StartedAt: 2016-09-20 04:33:24 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 04:35:56 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 151.7 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_1.7.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ClassifyR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.7.4’
* 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’
errorMap,list: no visible binding for global variable ‘Class’
errorMap,list: no visible binding for global variable ‘name’
errorMap,list: no visible binding for global variable ‘type’
errorMap,list: no visible binding for global variable ‘Error’
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’
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 Error Freq 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       10.017  0.213  14.738
runTest                     9.248  0.185   9.439
distribution                9.126  0.209  12.390
edgeRselection              8.837  0.302   9.168
runTests                    8.495  0.131  11.535
DMDselection                7.537  0.163   7.705
likelihoodRatioSelection    7.343  0.108   7.453
KullbackLeiblerSelection    6.901  0.104   7.010
KolmogorovSmirnovSelection  6.522  0.134   6.663
* 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-3.4-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	10.017	0.213	14.738
DMDselection	7.537	0.163	7.705
KolmogorovSmirnovSelection	6.522	0.134	6.663
KullbackLeiblerSelection	6.901	0.104	7.010
PredictParams-class	0.004	0.001	0.004
ROCplot	0.384	0.002	0.386
ResubstituteParams-class	0.001	0.000	0.001
SelectParams-class	0.009	0.001	0.010
SelectResult-class	0.002	0.000	0.001
TrainParams-class	0.010	0.001	0.010
TransformParams-class	0.002	0.000	0.002
bartlettSelection	0.672	0.006	0.677
calcPerformance	0.005	0.000	0.005
classifyInterface	0.493	0.093	0.599
distribution	9.126	0.209	12.390
edgeRselection	8.837	0.302	9.168
errorMap	0.901	0.010	0.912
fisherDiscriminant	0.048	0.000	0.048
functionOrList-class	0.008	0.001	0.008
getLocationsAndScales	0.045	0.001	0.046
leveneSelection	1.739	0.018	1.818
likelihoodRatioSelection	7.343	0.108	7.453
limmaSelection	0.633	0.005	0.639
medianDifferenceSelection	0.564	0.004	0.568
mixmodels	2.839	0.014	2.906
naiveBayesKernel	0.516	0.030	0.546
nearestShrunkenCentroidPredictInterface	0.185	0.005	0.235
nearestShrunkenCentroidSelectionInterface	0.124	0.001	0.125
nearestShrunkenCentroidTrainInterface	0.112	0.002	0.115
pamrtrained-class	0.081	0.003	0.086
performancePlot	0.594	0.004	0.597
plotFeatureClasses	2.791	0.037	2.831
previousSelection	0.126	0.072	4.814
rankingPlot	1.373	0.129	3.239
runTest	9.248	0.185	9.439
runTests	8.495	0.131	11.535
selectionPlot	1.613	0.142	3.442
subtractFromLocation	0.027	0.001	0.027