BioC 3.4: CHECK report for ClassifyR on morelia

Package: ClassifyR

Version: 1.8.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.8.2.tar.gz

StartedAt: 2017-04-14 23:58:13 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-15 00:01:20 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 186.7 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_1.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ClassifyR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.2’
* 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’
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       11.743  0.273  17.495
edgeRselection             11.094  0.296  11.522
runTest                    10.799  0.245  11.055
distribution                9.783  0.233  12.961
runTests                    9.548  0.164  13.433
DMDselection                9.195  0.136  10.557
KolmogorovSmirnovSelection  7.758  0.117   8.012
likelihoodRatioSelection    7.546  0.144   7.697
KullbackLeiblerSelection    7.020  0.084   7.111
previousSelection           0.155  0.078   5.892
* 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	11.743	0.273	17.495
DMDselection	9.195	0.136	10.557
KolmogorovSmirnovSelection	7.758	0.117	8.012
KullbackLeiblerSelection	7.020	0.084	7.111
PredictParams-class	0.004	0.000	0.003
ROCplot	0.665	0.010	0.676
ResubstituteParams-class	0.002	0.000	0.002
SelectParams-class	0.009	0.000	0.010
SelectResult-class	0.001	0.000	0.001
TrainParams-class	0.009	0.001	0.010
TransformParams-class	0.001	0.000	0.001
bartlettSelection	1.007	0.003	1.012
calcPerformance	0.009	0.000	0.009
classifyInterface	0.504	0.068	0.606
distribution	9.783	0.233	12.961
edgeRselection	11.094	0.296	11.522
errorMap	1.202	0.026	1.228
fisherDiscriminant	0.041	0.001	0.041
functionOrList-class	0.009	0.001	0.009
getLocationsAndScales	0.052	0.003	0.085
leveneSelection	1.772	0.040	1.925
likelihoodRatioSelection	7.546	0.144	7.697
limmaSelection	0.675	0.007	0.682
medianDifferenceSelection	0.756	0.006	0.763
mixmodels	3.319	0.017	4.059
naiveBayesKernel	0.479	0.013	0.493
nearestShrunkenCentroidPredictInterface	0.152	0.006	0.429
nearestShrunkenCentroidSelectionInterface	0.129	0.002	0.131
nearestShrunkenCentroidTrainInterface	0.112	0.004	0.116
pamrtrained-class	0.065	0.000	0.067
performancePlot	0.759	0.004	0.859
plotFeatureClasses	3.279	0.007	3.801
previousSelection	0.155	0.078	5.892
rankingPlot	1.458	0.160	3.976
runTest	10.799	0.245	11.055
runTests	9.548	0.164	13.433
selectionPlot	2.375	0.205	4.609
subtractFromLocation	0.048	0.001	0.049