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BioC 3.2: CHECK report for ClassifyR on zin1

This page was generated on 2016-04-23 10:14:01 -0700 (Sat, 23 Apr 2016).

Package 177/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 1.4.15
Dario Strbenac
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ClassifyR
Last Changed Rev: 114330 / Revision: 116712
Last Changed Date: 2016-03-07 15:00:02 -0800 (Mon, 07 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 1.4.15
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.4.15.tar.gz
StartedAt: 2016-04-22 23:11:02 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:13:19 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 137.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.4.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/ClassifyR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.4.15’
* 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/3s] 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 ... NOTE
TrainParams,ANY : .local: no visible binding for global variable ‘dlda’
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> : <anonymous>:
  no visible binding for global variable ‘classes’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  ‘largerClass’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  ‘classes’
naiveBayesKernel,ExpressionSet : .local: no visible binding for global
  variable ‘featureValues’
performancePlot,list : .local: no visible binding for global variable
  ‘Freq’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
  binding for global variable ‘expr’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
  binding for global variable ‘..density..’
selectionPlot,list : .local: no visible binding for global variable
  ‘Freq’
* 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 ... [108s/99s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
distribution               11.628  0.244  10.279
ClassifyResult-class        9.281  0.172   9.710
runTest                     8.932  0.092   9.038
edgeRselection              8.875  0.135   9.086
DMDselection                8.101  0.124   6.597
runTests                    7.303  0.052   9.397
likelihoodRatioSelection    6.798  0.020   6.840
KolmogorovSmirnovSelection  6.734  0.008   6.739
KullbackLeiblerSelection    6.710  0.012   6.717
selectionPlot               5.697  0.725   2.451
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.


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-class9.2810.1729.710
DMDselection8.1010.1246.597
KolmogorovSmirnovSelection6.7340.0086.739
KullbackLeiblerSelection6.7100.0126.717
PredictParams-class0.0020.0000.002
ROCplot0.6260.0040.630
ResubstituteParams-class0.0030.0000.002
SelectParams-class0.0160.0000.017
SelectResult-class0.0020.0000.002
TrainParams-class0.0110.0000.011
TransformParams-class0.0010.0000.002
bartlettSelection0.9600.0000.967
calcPerformance0.0060.0000.006
classifyInterface0.7950.0080.816
distribution11.628 0.24410.279
edgeRselection8.8750.1359.086
errorMap0.7580.0000.757
fisherDiscriminant0.0350.0000.035
functionOrList-class0.0020.0040.006
getLocationsAndScales0.0340.0000.034
leveneSelection3.2650.0083.276
likelihoodRatioSelection6.7980.0206.840
limmaSelection0.5920.0000.593
mixmodels4.6700.0084.755
naiveBayesKernel0.4980.0320.541
nearestShrunkenCentroidPredictInterface0.1610.0040.165
nearestShrunkenCentroidSelectionInterface0.1450.0000.144
nearestShrunkenCentroidTrainInterface0.1100.0000.111
pamrtrained-class0.0610.0000.060
performancePlot0.6630.0040.667
plotFeatureClasses2.2320.0002.230
previousSelection3.6400.4693.044
rankingPlot4.0000.9242.105
runTest8.9320.0929.038
runTests7.3030.0529.397
selectionPlot5.6970.7252.451
subtractFromLocation0.0370.0000.037