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BioC 3.0: CHECK report for ClassifyR on oaxaca

This page was generated on 2015-04-10 10:09:09 -0700 (Fri, 10 Apr 2015).

Package 158/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 1.0.18
Dario Strbenac
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ClassifyR
Last Changed Rev: 100630 / Revision: 102249
Last Changed Date: 2015-03-12 23:01:05 -0700 (Thu, 12 Mar 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

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

Command output

##############################################################################
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### Running command:
###
###   /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

ClassifyR.Rcheck/00install.out:

* 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)

ClassifyR.Rcheck/ClassifyR-Ex.timings:

nameusersystemelapsed
ClassifyResult-class11.043 0.19414.081
DMDselection0.8200.0330.854
KolmogorovSmirnovSelection0.7600.0080.768
KullbackLeiblerSelection0.8240.0050.828
PredictParams-class0.0040.0010.004
ResubstituteParams-class0.0030.0000.003
SelectionParams-class0.0060.0010.007
TrainParams-class0.0190.0010.020
TransformParams-class0.0040.0000.004
calcPerformance0.0080.0000.008
classifyInterface0.5510.1190.684
distribution15.197 0.58813.325
edgeRselection25.143 0.66626.175
errorMap0.0050.0000.005
fisherDiscriminant0.0510.0010.052
functionOrList-class0.0080.0010.014
getLocationsAndScales0.0530.0010.064
leveneSelection4.7710.0754.941
likelihoodRatioSelection1.0300.0071.038
limmaSelection0.9070.0040.911
mixmodels7.2100.0627.353
naiveBayesKernel0.3560.0150.372
nearestShrunkenCentroidPredictInterface0.2710.0160.299
nearestShrunkenCentroidSelectionInterface0.2300.0050.253
nearestShrunkenCentroidTrainInterface0.1700.0060.177
pamrtrained-class0.0900.0010.092
plotFeatureClasses0.0030.0000.003
rankPlot0.0060.0000.006
runTest11.529 0.20311.823
runTests14.336 0.55813.143
selectionPlot0.0050.0010.006
subtractFromLocation0.0600.0350.096