BioC 3.2: CHECK report for ClassifyR on perceval

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 23:13:00 -0700 (Sun, 23 Aug 2015)

EndedAt: 2015-08-23 23:16:01 -0700 (Sun, 23 Aug 2015)

EllapsedTime: 181.1 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_1.3.13.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ClassifyR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [5s/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
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’
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’
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’
TrainParams,ANY : .local: no visible binding for global variable ‘dlda’
* 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 ... [124s/119s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ClassifyResult-class 13.066  1.015  15.675
edgeRselection       13.012  0.515  13.549
runTests             12.161  0.425  12.593
distribution         11.650  0.498  12.169
runTest              11.072  0.481  11.560
selectionPlot         6.325  4.438   7.459
rankingPlot           6.501  4.063   7.616
mixmodels             6.420  0.110   6.588
leveneSelection       4.733  0.135   5.042
* 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	13.066	1.015	15.675
DMDselection	2.622	0.050	2.680
KolmogorovSmirnovSelection	2.698	0.068	2.768
KullbackLeiblerSelection	2.591	0.038	2.630
PredictParams-class	0.003	0.000	0.004
ROCplot	0.925	0.018	0.943
ResubstituteParams-class	0.003	0.000	0.004
SelectParams-class	0.010	0.001	0.011
SelectResult-class	0.002	0.000	0.002
TrainParams-class	0.035	0.001	0.035
TransformParams-class	0.002	0.000	0.002
bartlettSelection	1.290	0.006	1.298
calcPerformance	0.009	0.000	0.009
classifyInterface	0.976	0.190	1.182
distribution	11.650	0.498	12.169
edgeRselection	13.012	0.515	13.549
errorMap	0.006	0.000	0.006
fisherDiscriminant	0.047	0.000	0.048
functionOrList-class	0.007	0.001	0.008
getLocationsAndScales	0.046	0.002	0.047
leveneSelection	4.733	0.135	5.042
likelihoodRatioSelection	3.133	0.078	3.216
limmaSelection	0.957	0.006	0.964
mixmodels	6.420	0.110	6.588
naiveBayesKernel	0.352	0.001	0.354
nearestShrunkenCentroidPredictInterface	0.319	0.007	0.342
nearestShrunkenCentroidSelectionInterface	0.294	0.003	0.297
nearestShrunkenCentroidTrainInterface	0.257	0.005	0.263
pamrtrained-class	0.085	0.003	0.089
performancePlot	0.595	0.005	0.600
plotFeatureClasses	3.212	0.016	3.233
previousSelection	3.894	0.008	3.904
rankingPlot	6.501	4.063	7.616
runTest	11.072	0.481	11.560
runTests	12.161	0.425	12.593
selectionPlot	6.325	4.438	7.459
subtractFromLocation	0.048	0.014	0.062