BioC 3.5: CHECK report for ClassifyR on oaxaca

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: 2017-03-04 00:38:29 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 00:42:04 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 214.5 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 r72177)
* 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
selectionPlot              43.507  7.965   5.086
edgeRselection             11.929  0.318  14.031
distribution               11.458  0.299  16.997
runTest                    10.586  0.188  10.780
runTests                    9.495  0.208  13.802
ClassifyResult-class        9.205  0.226  17.750
KullbackLeiblerSelection    8.714  0.044  10.294
DMDselection                8.303  0.209   8.513
KolmogorovSmirnovSelection  8.223  0.089   8.938
likelihoodRatioSelection    7.612  0.117   7.733
plotFeatureClasses          4.253  0.015   6.608
previousSelection           0.163  0.094   7.315
* 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	9.205	0.226	17.750
DMDselection	8.303	0.209	8.513
KolmogorovSmirnovSelection	8.223	0.089	8.938
KullbackLeiblerSelection	8.714	0.044	10.294
PredictParams-class	0.004	0.000	0.004
ROCplot	3.603	0.009	4.357
ResubstituteParams-class	0.003	0.000	0.003
SelectParams-class	0.019	0.001	0.022
SelectResult-class	0.001	0.000	0.002
TrainParams-class	0.011	0.000	0.014
TransformParams-class	0.003	0.000	0.002
bartlettSelection	1.480	0.014	1.734
calcPerformance	0.009	0.001	0.009
classifyInterface	0.552	0.073	0.702
distribution	11.458	0.299	16.997
edgeRselection	11.929	0.318	14.031
fisherDiscriminant	0.032	0.000	0.032
functionOrList-class	0.005	0.001	0.005
getLocationsAndScales	0.027	0.001	0.027
leveneSelection	2.803	0.055	3.870
likelihoodRatioSelection	7.612	0.117	7.733
limmaSelection	1.007	0.023	1.031
medianDifferenceSelection	0.598	0.003	0.601
mixmodels	4.082	0.021	4.337
naiveBayesKernel	0.568	0.010	0.579
nearestShrunkenCentroidPredictInterface	0.265	0.006	0.376
nearestShrunkenCentroidSelectionInterface	0.460	0.004	0.463
nearestShrunkenCentroidTrainInterface	0.097	0.002	0.099
pamrtrained-class	0.067	0.001	0.068
performancePlot	2.020	0.024	2.097
plotFeatureClasses	4.253	0.015	6.608
previousSelection	0.163	0.094	7.315
rankingPlot	1.790	0.174	4.349
runTest	10.586	0.188	10.780
runTests	9.495	0.208	13.802
samplesMetricMap	1.343	0.134	1.538
selectionPlot	43.507	7.965	5.086
subtractFromLocation	0.078	0.001	0.078