BioC 3.0: CHECK report for ClassifyR on oaxaca

Package: ClassifyR

Version: 1.0.18

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ClassifyR_1.0.18.tar.gz

StartedAt: 2015-04-09 22:19:17 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:22:05 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 167.9 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 --no-multiarch ClassifyR_1.0.18.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ClassifyR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.0.18’
* 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/9s] 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 ... OK
* 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 ... [106s/100s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
edgeRselection       25.143  0.666  26.175
distribution         15.197  0.588  13.325
runTests             14.336  0.558  13.143
runTest              11.529  0.203  11.823
ClassifyResult-class 11.043  0.194  14.081
mixmodels             7.210  0.062   7.353
* 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

* 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	11.043	0.194	14.081
DMDselection	0.820	0.033	0.854
KolmogorovSmirnovSelection	0.760	0.008	0.768
KullbackLeiblerSelection	0.824	0.005	0.828
PredictParams-class	0.004	0.001	0.004
ResubstituteParams-class	0.003	0.000	0.003
SelectionParams-class	0.006	0.001	0.007
TrainParams-class	0.019	0.001	0.020
TransformParams-class	0.004	0.000	0.004
calcPerformance	0.008	0.000	0.008
classifyInterface	0.551	0.119	0.684
distribution	15.197	0.588	13.325
edgeRselection	25.143	0.666	26.175
errorMap	0.005	0.000	0.005
fisherDiscriminant	0.051	0.001	0.052
functionOrList-class	0.008	0.001	0.014
getLocationsAndScales	0.053	0.001	0.064
leveneSelection	4.771	0.075	4.941
likelihoodRatioSelection	1.030	0.007	1.038
limmaSelection	0.907	0.004	0.911
mixmodels	7.210	0.062	7.353
naiveBayesKernel	0.356	0.015	0.372
nearestShrunkenCentroidPredictInterface	0.271	0.016	0.299
nearestShrunkenCentroidSelectionInterface	0.230	0.005	0.253
nearestShrunkenCentroidTrainInterface	0.170	0.006	0.177
pamrtrained-class	0.090	0.001	0.092
plotFeatureClasses	0.003	0.000	0.003
rankPlot	0.006	0.000	0.006
runTest	11.529	0.203	11.823
runTests	14.336	0.558	13.143
selectionPlot	0.005	0.001	0.006
subtractFromLocation	0.060	0.035	0.096