BioC 3.1: CHECK report for ClassifyR on morelia

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: 2015-10-09 00:18:29 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:21:08 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 158.8 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 (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 ‘1.2.4’
* 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 ... [3s/27s] OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
* 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
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’
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>: 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’
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’
* 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 ... [87s/85s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
edgeRselection       16.016  1.294  17.446
distribution         12.227  0.993  11.305
ClassifyResult-class 11.622  1.124  12.765
runTest               9.446  0.537   9.992
runTests              8.677  0.454  12.831
mixmodels             6.251  0.244   6.628
leveneSelection       3.619  0.393   5.981
* 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: 3 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	11.622	1.124	12.765
DMDselection	0.73	0.04	0.77
KolmogorovSmirnovSelection	0.715	0.027	0.744
KullbackLeiblerSelection	0.778	0.035	0.815
PredictParams-class	0.004	0.000	0.004
ROCplot	0.639	0.041	0.681
ResubstituteParams-class	0.003	0.001	0.003
SelectionParams-class	0.006	0.000	0.007
TrainParams-class	0.015	0.000	0.017
TransformParams-class	0.005	0.002	0.007
calcPerformance	0.012	0.004	0.016
classifyInterface	0.509	0.152	0.679
distribution	12.227	0.993	11.305
edgeRselection	16.016	1.294	17.446
errorMap	0.003	0.000	0.003
fisherDiscriminant	0.045	0.001	0.045
functionOrList-class	0.005	0.000	0.005
getLocationsAndScales	0.029	0.001	0.030
leveneSelection	3.619	0.393	5.981
likelihoodRatioSelection	0.885	0.084	0.970
limmaSelection	0.769	0.032	0.799
mixmodels	6.251	0.244	6.628
naiveBayesKernel	0.232	0.007	0.241
nearestShrunkenCentroidPredictInterface	0.184	0.004	0.233
nearestShrunkenCentroidSelectionInterface	0.132	0.001	0.134
nearestShrunkenCentroidTrainInterface	0.125	0.002	0.128
pamrtrained-class	0.070	0.001	0.071
performancePlot	0.304	0.031	0.336
plotFeatureClasses	0.003	0.002	0.005
rankPlot	0.004	0.000	0.004
runTest	9.446	0.537	9.992
runTests	8.677	0.454	12.831
selectionPlot	0.004	0.000	0.004
subtractFromLocation	0.045	0.022	0.067