BioC 3.4: CHECK report for ClassifyR on malbec1

Package: ClassifyR

Version: 1.8.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.8.2.tar.gz

StartedAt: 2017-04-14 21:35:47 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 21:38:06 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 139.8 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ClassifyR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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
runTest                  10.188  0.108  10.304
ClassifyResult-class      9.568  0.136  12.628
edgeRselection            9.244  0.096   9.358
distribution              8.328  0.064  10.791
runTests                  7.028  0.060   9.842
likelihoodRatioSelection  6.088  0.012   6.103
DMDselection              5.752  0.036   5.794
KullbackLeiblerSelection  5.080  0.008   5.092
previousSelection         0.140  0.048   5.951
* 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
  ‘/home/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	9.568	0.136	12.628
DMDselection	5.752	0.036	5.794
KolmogorovSmirnovSelection	4.844	0.008	4.854
KullbackLeiblerSelection	5.080	0.008	5.092
PredictParams-class	0.004	0.000	0.002
ROCplot	0.464	0.000	0.462
ResubstituteParams-class	0.000	0.000	0.001
SelectParams-class	0.008	0.004	0.009
SelectResult-class	0	0	0
TrainParams-class	0.008	0.000	0.006
TransformParams-class	0.000	0.000	0.001
bartlettSelection	0.776	0.000	0.778
calcPerformance	0.008	0.000	0.005
classifyInterface	0.560	0.020	0.589
distribution	8.328	0.064	10.791
edgeRselection	9.244	0.096	9.358
errorMap	0.720	0.012	0.733
fisherDiscriminant	0.032	0.000	0.034
functionOrList-class	0.004	0.000	0.005
getLocationsAndScales	0.084	0.000	0.084
leveneSelection	1.644	0.000	1.644
likelihoodRatioSelection	6.088	0.012	6.103
limmaSelection	0.448	0.000	0.448
medianDifferenceSelection	0.448	0.004	0.452
mixmodels	2.224	0.000	2.285
naiveBayesKernel	0.428	0.004	0.434
nearestShrunkenCentroidPredictInterface	0.12	0.00	0.12
nearestShrunkenCentroidSelectionInterface	0.112	0.000	0.112
nearestShrunkenCentroidTrainInterface	0.076	0.000	0.074
pamrtrained-class	0.048	0.000	0.047
performancePlot	0.904	0.000	0.906
plotFeatureClasses	2.460	0.004	2.465
previousSelection	0.140	0.048	5.951
rankingPlot	1.444	0.092	3.694
runTest	10.188	0.108	10.304
runTests	7.028	0.060	9.842
selectionPlot	1.352	0.076	3.179
subtractFromLocation	0.024	0.000	0.027