BioC 3.1: CHECK report for ClassifyR on zin2

Package: ClassifyR

Version: 1.2.4

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.2.4.tar.gz

StartedAt: 2015-10-08 23:32:48 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:34:57 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 128.1 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.2.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/ClassifyR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.4’
* 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/4s] 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
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 ... [70s/80s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
edgeRselection       18.563  0.114  22.581
distribution         10.886  0.248  12.058
ClassifyResult-class  7.737  0.099  12.323
runTest               6.418  0.036   6.506
runTests              6.104  0.078   9.886
* 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
  ‘/home/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	7.737	0.099	12.323
DMDselection	3.817	0.156	0.984
KolmogorovSmirnovSelection	0.513	0.004	0.626
KullbackLeiblerSelection	0.574	0.004	0.760
PredictParams-class	0.002	0.000	0.003
ROCplot	0.604	0.008	0.719
ResubstituteParams-class	0.002	0.000	0.002
SelectionParams-class	0.004	0.000	0.004
TrainParams-class	0.011	0.000	0.010
TransformParams-class	0.002	0.000	0.003
calcPerformance	0.008	0.000	0.007
classifyInterface	0.767	0.016	0.922
distribution	10.886	0.248	12.058
edgeRselection	18.563	0.114	22.581
errorMap	0.004	0.000	0.003
fisherDiscriminant	0.035	0.000	0.060
functionOrList-class	0.002	0.004	0.015
getLocationsAndScales	0.033	0.000	0.033
leveneSelection	2.738	0.004	3.017
likelihoodRatioSelection	0.658	0.000	0.794
limmaSelection	0.847	0.004	1.066
mixmodels	3.428	0.008	4.546
naiveBayesKernel	0.245	0.004	0.256
nearestShrunkenCentroidPredictInterface	0.142	0.012	0.160
nearestShrunkenCentroidSelectionInterface	0.125	0.007	0.150
nearestShrunkenCentroidTrainInterface	0.100	0.004	0.107
pamrtrained-class	0.066	0.000	0.068
performancePlot	0.219	0.000	0.224
plotFeatureClasses	0.002	0.000	0.003
rankPlot	0.003	0.000	0.004
runTest	6.418	0.036	6.506
runTests	6.104	0.078	9.886
selectionPlot	0.004	0.000	0.012
subtractFromLocation	3.396	0.386	0.075