BioC 3.1: CHECK report for ClassifyR on petty

Package: ClassifyR

Version: 1.2.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.2.4.tar.gz

StartedAt: 2015-10-08 22:05:19 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 22:08:41 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 201.4 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_1.2.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.2.4’
* 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 ... [6s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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>: no visible
  binding for global variable ‘classes’
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’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
  binding for global variable ‘expr’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
  binding for global variable ‘..density..’
rankPlot,list : .local: no visible binding for global variable ‘top’
rankPlot,list : .local: no visible binding for global variable
  ‘overlap’
rankPlot,list : .local: no visible binding for global variable
  ‘validation’
rankPlot,list : .local: no visible binding for global variable
  ‘dataset’
rankPlot,list : .local: no visible binding for global variable
  ‘analysis’
rankPlot,list : .local: no visible global function definition for
  ‘theme’
rankPlot,list : .local: no visible global function definition for
  ‘element_text’
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 ‘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 global function definition for
  ‘theme’
selectionPlot,list : .local: no visible global function definition for
  ‘element_text’
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 ... [135s/125s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
edgeRselection       27.788  1.564  29.429
runTests             20.395  2.670  18.461
ClassifyResult-class 20.486  1.042  18.474
distribution         17.257  0.784  18.399
runTest              12.917  0.264  13.219
mixmodels             7.952  0.085   8.110
leveneSelection       5.416  0.088   5.645
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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	20.486	1.042	18.474
DMDselection	1.407	0.091	1.499
KolmogorovSmirnovSelection	0.899	0.005	0.904
KullbackLeiblerSelection	1.029	0.004	1.033
PredictParams-class	0.005	0.000	0.005
ROCplot	1.016	0.013	1.030
ResubstituteParams-class	0.005	0.001	0.005
SelectionParams-class	0.010	0.001	0.011
TrainParams-class	0.050	0.000	0.051
TransformParams-class	0.005	0.000	0.005
calcPerformance	0.016	0.000	0.017
classifyInterface	1.188	0.195	1.399
distribution	17.257	0.784	18.399
edgeRselection	27.788	1.564	29.429
errorMap	0.005	0.000	0.005
fisherDiscriminant	0.048	0.001	0.049
functionOrList-class	0.007	0.001	0.009
getLocationsAndScales	0.045	0.001	0.046
leveneSelection	5.416	0.088	5.645
likelihoodRatioSelection	1.440	0.006	1.448
limmaSelection	0.943	0.003	0.946
mixmodels	7.952	0.085	8.110
naiveBayesKernel	0.406	0.002	0.408
nearestShrunkenCentroidPredictInterface	0.377	0.005	0.399
nearestShrunkenCentroidSelectionInterface	0.357	0.003	0.361
nearestShrunkenCentroidTrainInterface	0.325	0.003	0.329
pamrtrained-class	0.113	0.001	0.115
performancePlot	0.472	0.002	0.475
plotFeatureClasses	0.003	0.000	0.004
rankPlot	0.006	0.000	0.007
runTest	12.917	0.264	13.219
runTests	20.395	2.670	18.461
selectionPlot	0.009	0.004	0.013
subtractFromLocation	0.093	0.039	0.132