BioC 3.3: CHECK report for ClassifyR on oaxaca

Package: ClassifyR

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.6.2.tar.gz

StartedAt: 2016-10-13 00:15:00 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 00:18:22 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 202.1 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_1.6.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘1.6.2’
* 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’
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 binding for global variable ‘Freq’
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
rankingPlot                19.234  3.040   3.706
ClassifyResult-class       10.670  0.226  14.748
runTest                    10.355  0.229  10.603
edgeRselection              9.739  0.346  10.168
distribution                9.819  0.218  12.851
runTests                    9.439  0.157  13.042
likelihoodRatioSelection    8.498  0.106   8.625
DMDselection                8.311  0.169   8.509
KolmogorovSmirnovSelection  8.232  0.091   8.448
KullbackLeiblerSelection    7.460  0.084   7.557
previousSelection           0.150  0.078   5.182
* 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-3.3-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	10.670	0.226	14.748
DMDselection	8.311	0.169	8.509
KolmogorovSmirnovSelection	8.232	0.091	8.448
KullbackLeiblerSelection	7.460	0.084	7.557
PredictParams-class	0.003	0.000	0.003
ROCplot	0.687	0.011	0.719
ResubstituteParams-class	0.002	0.000	0.003
SelectParams-class	0.017	0.001	0.018
SelectResult-class	0.002	0.001	0.001
TrainParams-class	0.010	0.000	0.011
TransformParams-class	0.001	0.000	0.001
bartlettSelection	1.053	0.003	1.057
calcPerformance	0.008	0.000	0.008
classifyInterface	0.531	0.070	0.645
distribution	9.819	0.218	12.851
edgeRselection	9.739	0.346	10.168
errorMap	1.056	0.003	1.062
fisherDiscriminant	0.051	0.000	0.052
functionOrList-class	0.007	0.000	0.008
getLocationsAndScales	0.045	0.002	0.046
leveneSelection	3.925	0.036	4.091
likelihoodRatioSelection	8.498	0.106	8.625
limmaSelection	0.726	0.003	0.730
mixmodels	3.667	0.022	3.720
naiveBayesKernel	0.548	0.007	0.558
nearestShrunkenCentroidPredictInterface	0.197	0.005	0.233
nearestShrunkenCentroidSelectionInterface	0.178	0.002	0.180
nearestShrunkenCentroidTrainInterface	0.120	0.002	0.123
pamrtrained-class	0.081	0.001	0.082
performancePlot	0.874	0.005	0.899
plotFeatureClasses	3.161	0.009	3.497
previousSelection	0.150	0.078	5.182
rankingPlot	19.234	3.040	3.706
runTest	10.355	0.229	10.603
runTests	9.439	0.157	13.042
selectionPlot	1.853	0.125	3.926
subtractFromLocation	0.040	0.001	0.041