BioC 3.3: CHECK report for ClassifyR on morelia

Package: ClassifyR

Version: 1.5.15

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.5.15.tar.gz

StartedAt: 2016-04-21 00:28:16 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 00:31:21 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 185.4 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_1.5.15.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ClassifyR.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.5.15’
* 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 ... [4s/5s] 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 ... [144s/130s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
runTest                    11.298  0.233  11.580
ClassifyResult-class       10.670  0.214  13.587
distribution               10.203  0.235  13.232
runTests                   10.043  0.169  13.840
edgeRselection              8.049  0.313   8.507
KullbackLeiblerSelection    8.045  0.128   8.183
KolmogorovSmirnovSelection  8.043  0.125   8.175
likelihoodRatioSelection    7.690  0.103   7.800
DMDselection                6.682  0.186   7.192
mixmodels                   5.745  0.050   6.020
previousSelection           0.148  0.074   5.655
* 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	0.214	13.587
DMDselection	6.682	0.186	7.192
KolmogorovSmirnovSelection	8.043	0.125	8.175
KullbackLeiblerSelection	8.045	0.128	8.183
PredictParams-class	0.003	0.000	0.003
ROCplot	0.761	0.015	1.058
ResubstituteParams-class	0.002	0.000	0.002
SelectParams-class	0.015	0.000	0.015
SelectResult-class	0.001	0.000	0.002
TrainParams-class	0.009	0.000	0.009
TransformParams-class	0.002	0.000	0.001
bartlettSelection	1.267	0.007	1.277
calcPerformance	0.009	0.001	0.009
classifyInterface	0.529	0.100	0.652
distribution	10.203	0.235	13.232
edgeRselection	8.049	0.313	8.507
errorMap	1.178	0.003	1.182
fisherDiscriminant	0.040	0.001	0.040
functionOrList-class	0.008	0.001	0.009
getLocationsAndScales	0.046	0.001	0.046
leveneSelection	3.773	0.080	4.730
likelihoodRatioSelection	7.690	0.103	7.800
limmaSelection	0.827	0.003	0.831
mixmodels	5.745	0.050	6.020
naiveBayesKernel	0.521	0.016	0.537
nearestShrunkenCentroidPredictInterface	0.162	0.007	0.851
nearestShrunkenCentroidSelectionInterface	0.196	0.003	0.199
nearestShrunkenCentroidTrainInterface	0.118	0.002	0.133
pamrtrained-class	0.081	0.002	0.082
performancePlot	0.743	0.007	1.008
plotFeatureClasses	3.245	0.020	3.689
previousSelection	0.148	0.074	5.655
rankingPlot	1.772	0.143	3.961
runTest	11.298	0.233	11.580
runTests	10.043	0.169	13.840
selectionPlot	2.052	0.176	4.241
subtractFromLocation	0.043	0.001	0.044