BioC 3.0: CHECK report for ClassifyR on zin1

Package: ClassifyR

Version: 1.0.18

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.0.18.tar.gz

StartedAt: 2015-04-09 22:37:23 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:39:24 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 121.4 seconds

RetCode: 0

Status:  OK

CheckDir: ClassifyR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.0.18.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/ClassifyR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-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 ‘1.0.18’
* 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 ... [4s/4s] 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 ... [81s/77s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
edgeRselection       22.677  0.128  22.870
distribution         13.957  0.264  10.441
runTests             11.281  0.392   9.896
runTest               8.900  0.100   9.016
ClassifyResult-class  8.084  0.132  10.192
* 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	8.084	0.132	10.192
DMDselection	0.800	0.012	0.813
KolmogorovSmirnovSelection	0.640	0.008	0.652
KullbackLeiblerSelection	0.672	0.000	0.673
PredictParams-class	0.004	0.000	0.004
ResubstituteParams-class	0.004	0.000	0.002
SelectionParams-class	0.008	0.000	0.005
TrainParams-class	0.012	0.000	0.014
TransformParams-class	0.004	0.000	0.003
calcPerformance	0.008	0.000	0.008
classifyInterface	0.792	0.028	0.836
distribution	13.957	0.264	10.441
edgeRselection	22.677	0.128	22.870
errorMap	0.004	0.000	0.004
fisherDiscriminant	0.048	0.000	0.045
functionOrList-class	0.008	0.000	0.007
getLocationsAndScales	0.04	0.00	0.04
leveneSelection	3.572	0.016	3.629
likelihoodRatioSelection	0.781	0.004	0.786
limmaSelection	0.700	0.000	0.703
mixmodels	3.684	0.020	3.792
naiveBayesKernel	0.280	0.028	0.308
nearestShrunkenCentroidPredictInterface	0.212	0.016	0.229
nearestShrunkenCentroidSelectionInterface	0.164	0.000	0.165
nearestShrunkenCentroidTrainInterface	0.128	0.004	0.132
pamrtrained-class	0.076	0.000	0.076
plotFeatureClasses	0.004	0.000	0.002
rankPlot	0.004	0.000	0.005
runTest	8.900	0.100	9.016
runTests	11.281	0.392	9.896
selectionPlot	0.004	0.000	0.004
subtractFromLocation	0.048	0.000	0.047