BioC 3.0: CHECK report for ClassifyR on perceval

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 23:55:24 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:58:40 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 195.3 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-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 ‘1.0.18’
* 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 ... [7s/15s] 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 ... [118s/109s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
edgeRselection       37.635  1.164  38.846
distribution         16.366  1.574  12.174
runTests             10.448  0.724  11.652
runTest              10.251  0.314  10.582
ClassifyResult-class  8.589  0.272  11.972
mixmodels             6.567  0.099   6.710
leveneSelection       5.270  0.125   5.725
* 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	8.589	0.272	11.972
DMDselection	1.274	0.089	1.366
KolmogorovSmirnovSelection	0.810	0.009	0.821
KullbackLeiblerSelection	0.860	0.005	0.865
PredictParams-class	0.004	0.000	0.004
ResubstituteParams-class	0.002	0.001	0.003
SelectionParams-class	0.008	0.001	0.010
TrainParams-class	0.034	0.002	0.035
TransformParams-class	0.005	0.000	0.005
calcPerformance	0.009	0.000	0.009
classifyInterface	0.873	0.209	1.106
distribution	16.366	1.574	12.174
edgeRselection	37.635	1.164	38.846
errorMap	0.006	0.000	0.006
fisherDiscriminant	0.146	0.002	0.147
functionOrList-class	0.010	0.001	0.011
getLocationsAndScales	0.053	0.001	0.055
leveneSelection	5.270	0.125	5.725
likelihoodRatioSelection	1.014	0.006	1.020
limmaSelection	1.050	0.007	1.057
mixmodels	6.567	0.099	6.710
naiveBayesKernel	0.332	0.002	0.333
nearestShrunkenCentroidPredictInterface	0.360	0.016	0.409
nearestShrunkenCentroidSelectionInterface	0.327	0.007	0.336
nearestShrunkenCentroidTrainInterface	0.237	0.005	0.242
pamrtrained-class	0.093	0.003	0.095
plotFeatureClasses	0.003	0.000	0.003
rankPlot	0.007	0.001	0.006
runTest	10.251	0.314	10.582
runTests	10.448	0.724	11.652
selectionPlot	0.007	0.010	0.016
subtractFromLocation	0.092	0.076	0.169