BioC 3.2: CHECK report for ClassifyR on oaxaca

Package: ClassifyR

Version: 1.3.13

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.3.13.tar.gz

StartedAt: 2015-08-23 22:34:45 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 22:37:36 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 171.0 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_1.3.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ClassifyR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.3.13’
* 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/8s] 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
ROCplot,list : .local: no visible binding for global variable ‘FPR’
ROCplot,list : .local: no visible binding for global variable ‘TPR’
ROCplot,list : .local: no visible binding for global variable
  ‘validation’
ROCplot,list : .local: no visible binding for global variable
  ‘selection’
ROCplot,list : .local: no visible binding for global variable ‘dataset’
ROCplot,list : .local: no visible binding for global variable
  ‘analysis’
TrainParams,ANY : .local: no visible binding for global variable ‘dlda’
distribution,ClassifyResult : .local: no visible binding for global
  variable ‘..density..’
errorMap,list : .local: no visible binding for global variable ‘Class’
errorMap,list : .local: no visible binding for global variable ‘name’
errorMap,list : .local: no visible binding for global variable ‘type’
errorMap,list : .local: no visible binding for global variable ‘Error’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous>:
  no visible binding for global variable ‘classesSizes’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous>:
  no visible binding for global variable ‘classes’
performancePlot,list : .local: no visible binding for global variable
  ‘Freq’
performancePlot,list : .local: no visible binding for global variable
  ‘validation’
performancePlot,list : .local: no visible binding for global variable
  ‘dataset’
performancePlot,list : .local: no visible binding for global variable
  ‘analysis’
performancePlot,list : .local: no visible binding for global variable
  ‘selection’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
  binding for global variable ‘expr’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
  binding for global variable ‘..density..’
rankingPlot,list : .local: no visible binding for global variable ‘top’
rankingPlot,list : .local: no visible binding for global variable
  ‘overlap’
rankingPlot,list : .local: no visible binding for global variable
  ‘validation’
rankingPlot,list : .local: no visible binding for global variable
  ‘dataset’
rankingPlot,list : .local: no visible binding for global variable
  ‘analysis’
rankingPlot,list : .local: no visible binding for global variable
  ‘selection’
selectionPlot,list : .local: no visible binding for global variable
  ‘validation’
selectionPlot,list : .local: no visible binding for global variable
  ‘dataset’
selectionPlot,list : .local: no visible binding for global variable
  ‘analysis’
selectionPlot,list : .local: no visible binding for global variable
  ‘overlap’
selectionPlot,list : .local: no visible binding for global variable
  ‘size’
selectionPlot,list : .local: no visible binding for global variable
  ‘Freq’
* 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 ... [111s/110s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ClassifyResult-class 13.500  0.309  13.943
runTests             13.370  0.278  13.754
distribution         13.118  0.277  13.418
runTest              11.267  0.255  11.673
edgeRselection       10.323  0.268  10.674
mixmodels             6.997  0.057   7.135
rankingPlot           4.025  1.707   4.446
* 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-3.2-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	13.500	0.309	13.943
DMDselection	2.748	0.080	2.831
KolmogorovSmirnovSelection	2.778	0.067	2.864
KullbackLeiblerSelection	2.722	0.063	2.790
PredictParams-class	0.005	0.001	0.005
ROCplot	0.889	0.018	0.908
ResubstituteParams-class	0.003	0.000	0.003
SelectParams-class	0.007	0.001	0.008
SelectResult-class	0.002	0.000	0.002
TrainParams-class	0.017	0.001	0.017
TransformParams-class	0.002	0.000	0.002
bartlettSelection	1.220	0.003	1.232
calcPerformance	0.009	0.000	0.009
classifyInterface	0.537	0.077	0.625
distribution	13.118	0.277	13.418
edgeRselection	10.323	0.268	10.674
errorMap	0.005	0.000	0.006
fisherDiscriminant	0.049	0.000	0.050
functionOrList-class	0.009	0.001	0.010
getLocationsAndScales	0.050	0.002	0.051
leveneSelection	4.377	0.064	4.544
likelihoodRatioSelection	3.007	0.081	3.097
limmaSelection	0.844	0.004	0.849
mixmodels	6.997	0.057	7.135
naiveBayesKernel	0.366	0.003	0.372
nearestShrunkenCentroidPredictInterface	0.236	0.006	0.242
nearestShrunkenCentroidSelectionInterface	0.206	0.004	0.210
nearestShrunkenCentroidTrainInterface	0.170	0.004	0.175
pamrtrained-class	0.094	0.002	0.096
performancePlot	0.610	0.001	0.613
plotFeatureClasses	3.127	0.010	3.212
previousSelection	3.763	0.010	3.841
rankingPlot	4.025	1.707	4.446
runTest	11.267	0.255	11.673
runTests	13.370	0.278	13.754
selectionPlot	2.909	1.272	4.220
subtractFromLocation	0.057	0.005	0.062