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CHECK report for ClassifyR on riesling1

This page was generated on 2020-11-23 12:25:23 -0500 (Mon, 23 Nov 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE ClassifyR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 302/1907HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.11.0
Dario Strbenac
Snapshot Date: 2020-11-22 14:40:22 -0500 (Sun, 22 Nov 2020)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: master
Last Commit: e4a0740
Last Changed Date: 2020-10-27 10:58:03 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 2.11.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ClassifyR_2.11.0.tar.gz
StartedAt: 2020-11-22 19:46:49 -0500 (Sun, 22 Nov 2020)
EndedAt: 2020-11-22 19:57:15 -0500 (Sun, 22 Nov 2020)
EllapsedTime: 625.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ClassifyR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ClassifyR_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck'
* using R Under development (unstable) (2020-11-06 r79405)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ClassifyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ClassifyR' version '2.11.0'
* 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 whether package 'ClassifyR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: Previous alias or file overwritten by alias: easyHardClassifier
See 'D:/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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
.posterior_probs : <anonymous>: no visible global function definition
  for 'dmvnorm'
easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no
  visible binding for global variable 'measurements'
kTSPclassifier,DataFrame : <anonymous>: no visible global function
  definition for 'Pairs'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'measurement'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable '..density..'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'legends grouping'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'key'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'value'
plotFeatureClasses,DataFrame : <anonymous>: no visible binding for
  global variable 'ID'
rankingPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for 'first'
rankingPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for 'second'
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'first'
rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible
  global function definition for 'second'
runTest,DataFrame: no visible binding for global variable 'setsNodes'
runTestEasyHard,MultiAssayExperiment: no visible binding for global
  variable 'setsNodes'
runTests,DataFrame: no visible binding for global variable 'setsNodes'
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
  variable 'setsNodes'
runTestsEasyHard,MultiAssayExperiment: no visible binding for global
  variable '.iteration'
samplesMetricMap,list: no visible binding for global variable 'Class'
samplesMetricMap,list: no visible binding for global variable 'Group'
samplesMetricMap,list: no visible binding for global variable
  'measurements'
samplesMetricMap,list: no visible binding for global variable 'name'
samplesMetricMap,list: no visible binding for global variable 'type'
samplesMetricMap,list: no visible binding for global variable 'Metric'
samplesMetricMap,matrix: no visible binding for global variable 'Class'
samplesMetricMap,matrix: no visible binding for global variable 'Group'
samplesMetricMap,matrix: no visible binding for global variable
  'measurements'
samplesMetricMap,matrix: no visible binding for global variable 'name'
samplesMetricMap,matrix: no visible binding for global variable 'type'
samplesMetricMap,matrix: no visible binding for global variable
  'Metric'
selectionPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for 'first'
selectionPlot,list : <anonymous> : <anonymous>: no visible global
  function definition for 'second'
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for 'first'
selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no
  visible global function definition for 'second'
selectionPlot,list: no visible binding for global variable 'Freq'
Undefined global functions or variables:
  ..density.. .iteration Class Freq Group ID Metric Pairs dmvnorm first
  key legends grouping measurement measurements name second setsNodes
  type value
Consider adding
  importFrom("base", "grouping")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
ClassifyResult-class   5.87   0.12   39.52
runTests               2.04   0.25   38.36
selectionPlot          1.65   0.00    7.61
rankingPlot            1.36   0.03    7.50
distribution           1.08   0.13   24.53
previousSelection      1.05   0.02   19.62
previousTrained        0.98   0.03   20.78
elasticNetFeatures     0.67   0.00   14.03
elasticNetGLMinterface 0.50   0.01   13.73
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
ClassifyResult-class   6.86   0.27   47.05
runTests               2.17   0.17   40.82
selectionPlot          1.88   0.00    8.66
distribution           1.45   0.15   27.57
previousSelection      1.40   0.01   22.61
rankingPlot            1.35   0.00    7.36
previousTrained        1.28   0.00   21.54
elasticNetFeatures     1.00   0.00   21.66
elasticNetGLMinterface 0.78   0.04   19.33
* 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 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.



Installation output

ClassifyR.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/bioc/src/contrib/ClassifyR_2.11.0.tar.gz && rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ClassifyR.buildbin-libdir ClassifyR_2.11.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ClassifyR_2.11.0.zip && rm ClassifyR_2.11.0.tar.gz ClassifyR_2.11.0.zip
###
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##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1004k  100 1004k    0     0  33.8M      0 --:--:-- --:--:-- --:--:-- 33.8M

install for i386

* installing *source* package 'ClassifyR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ClassifyR'
    finding HTML links ... done
    ClassifyResult-class                    html  
REDIRECT:topic	 ClassifyResult -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 ClassifyResult-class -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 ClassifyResult,character,character,character,character,characterOrDataFrame-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 show,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 sampleNames -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 sampleNames,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 featureNames -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 featureNames,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 predictions -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 predictions,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 actualClasses -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 actualClasses,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 features -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 features,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 models -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 models,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 performance -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 performance,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 tunedParameters -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 tunedParameters,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 totalPredictions -> ClassifyResult-class.html [ SUCCESS ]
REDIRECT:topic	 totalPredictions,ClassifyResult-method -> ClassifyResult-class.html [ SUCCESS ]
    finding level-2 HTML links ... done

    DLDAinterface                           html  
REDIRECT:topic	 DLDAtrainInterface -> DLDAinterface.html [ SUCCESS ]
REDIRECT:topic	 DLDAtrainInterface,matrix-method -> DLDAinterface.html [ SUCCESS ]
REDIRECT:topic	 DLDAtrainInterface,DataFrame-method -> DLDAinterface.html [ SUCCESS ]
REDIRECT:topic	 DLDAtrainInterface,MultiAssayExperiment-method -> DLDAinterface.html [ SUCCESS ]
REDIRECT:topic	 DLDApredictInterface -> DLDAinterface.html [ SUCCESS ]
REDIRECT:topic	 DLDApredictInterface,dlda,matrix-method -> DLDAinterface.html [ SUCCESS ]
REDIRECT:topic	 DLDApredictInterface,dlda,DataFrame-method -> DLDAinterface.html [ SUCCESS ]
REDIRECT:topic	 DLDApredictInterface,dlda,MultiAssayExperiment-method -> DLDAinterface.html [ SUCCESS ]
REDIRECT:file	 DLDAinterface.html -> DLDAinterface.html [ SUCCESS ]
    DMDselection                            html  
REDIRECT:topic	 DMDselection -> DMDselection.html [ SUCCESS ]
REDIRECT:topic	 DMDselection,matrix-method -> DMDselection.html [ SUCCESS ]
REDIRECT:topic	 DMDselection,DataFrame-method -> DMDselection.html [ SUCCESS ]
REDIRECT:topic	 DMDselection,MultiAssayExperiment-method -> DMDselection.html [ SUCCESS ]
    EasyHardClassifier-class                html  
REDIRECT:topic	 EasyHardClassifier -> EasyHardClassifier-class.html [ SUCCESS ]
REDIRECT:topic	 EasyHardClassifier-class -> EasyHardClassifier-class.html [ SUCCESS ]
REDIRECT:topic	 EasyHardClassifier,listOrNULL,listOrCharacterOrNULL,character-method -> EasyHardClassifier-class.html [ SUCCESS ]
REDIRECT:topic	 show,EasyHardClassifier-method -> EasyHardClassifier-class.html [ SUCCESS ]
    FeatureSetCollection-class              html  
REDIRECT:topic	 FeatureSetCollection -> FeatureSetCollection-class.html [ SUCCESS ]
REDIRECT:topic	 FeatureSetCollection-class -> FeatureSetCollection-class.html [ SUCCESS ]
REDIRECT:topic	 FeatureSetCollection,list-method -> FeatureSetCollection-class.html [ SUCCESS ]
REDIRECT:topic	 length,FeatureSetCollection-method -> FeatureSetCollection-class.html [ SUCCESS ]
REDIRECT:topic	 show,FeatureSetCollection-method -> FeatureSetCollection-class.html [ SUCCESS ]
REDIRECT:topic	 [,FeatureSetCollection,integerOrNumeric,missing,ANY-method -> FeatureSetCollection-class.html [ SUCCESS ]
REDIRECT:topic	 [[,FeatureSetCollection,ANY,missing-method -> FeatureSetCollection-class.html [ SUCCESS ]
    FeatureSetCollectionOrNULL-class        html  
REDIRECT:topic	 FeatureSetCollectionOrNULL -> FeatureSetCollectionOrNULL-class.html [ SUCCESS ]
REDIRECT:topic	 FeatureSetCollectionOrNULL-class -> FeatureSetCollectionOrNULL-class.html [ SUCCESS ]
    KolmogorovSmirnovSelection              html  
REDIRECT:topic	 KolmogorovSmirnovSelection -> KolmogorovSmirnovSelection.html [ SUCCESS ]
REDIRECT:topic	 KolmogorovSmirnovSelection,matrix-method -> KolmogorovSmirnovSelection.html [ SUCCESS ]
REDIRECT:topic	 KolmogorovSmirnovSelection,DataFrame-method -> KolmogorovSmirnovSelection.html [ SUCCESS ]
REDIRECT:topic	 KolmogorovSmirnovSelection,MultiAssayExperiment-method -> KolmogorovSmirnovSelection.html [ SUCCESS ]
    KullbackLeiblerSelection                html  
REDIRECT:topic	 KullbackLeiblerSelection -> KullbackLeiblerSelection.html [ SUCCESS ]
REDIRECT:topic	 KullbackLeiblerSelection,matrix-method -> KullbackLeiblerSelection.html [ SUCCESS ]
REDIRECT:topic	 KullbackLeiblerSelection,DataFrame-method -> KullbackLeiblerSelection.html [ SUCCESS ]
REDIRECT:topic	 KullbackLeiblerSelection,MultiAssayExperiment-method -> KullbackLeiblerSelection.html [ SUCCESS ]
    MixModelsListsSet-class                 html  
REDIRECT:topic	 MixModelsListsSet -> MixModelsListsSet-class.html [ SUCCESS ]
REDIRECT:topic	 MixModelsListsSet-class -> MixModelsListsSet-class.html [ SUCCESS ]
REDIRECT:topic	 MixModelsListsSet,list-method -> MixModelsListsSet-class.html [ SUCCESS ]
    NSCpredictInterface                     html  
REDIRECT:topic	 NSCpredictInterface -> NSCpredictInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCpredictInterface,pamrtrained,matrix-method -> NSCpredictInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCpredictInterface,pamrtrained,DataFrame-method -> NSCpredictInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCpredictInterface,pamrtrained,MultiAssayExperiment-method -> NSCpredictInterface.html [ SUCCESS ]
    NSCselectionInterface                   html  
REDIRECT:topic	 NSCselectionInterface -> NSCselectionInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCselectionInterface,matrix-method -> NSCselectionInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCselectionInterface,DataFrame-method -> NSCselectionInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCselectionInterface,MultiAssayExperiment-method -> NSCselectionInterface.html [ SUCCESS ]
    NSCtrainInterface                       html  
REDIRECT:topic	 NSCtrainInterface -> NSCtrainInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCtrainInterface,matrix-method -> NSCtrainInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCtrainInterface,DataFrame-method -> NSCtrainInterface.html [ SUCCESS ]
REDIRECT:topic	 NSCtrainInterface,MultiAssayExperiment-method -> NSCtrainInterface.html [ SUCCESS ]
    PredictParams-class                     html  
REDIRECT:topic	 PredictParams -> PredictParams-class.html [ SUCCESS ]
REDIRECT:topic	 PredictParams-class -> PredictParams-class.html [ SUCCESS ]
REDIRECT:topic	 PredictParams,ANY-method -> PredictParams-class.html [ SUCCESS ]
REDIRECT:topic	 PredictParams,functionOrNULL-method -> PredictParams-class.html [ SUCCESS ]
    ROCplot                                 html  
REDIRECT:topic	 ROCplot -> ROCplot.html [ SUCCESS ]
REDIRECT:topic	 ROCplot,list-method -> ROCplot.html [ SUCCESS ]
    ResubstituteParams-class                html  
REDIRECT:topic	 ResubstituteParams -> ResubstituteParams-class.html [ SUCCESS ]
REDIRECT:topic	 ResubstituteParams-class -> ResubstituteParams-class.html [ SUCCESS ]
REDIRECT:topic	 ResubstituteParams,ANY,ANY,ANY-method -> ResubstituteParams-class.html [ SUCCESS ]
REDIRECT:topic	 ResubstituteParams,numeric,character,character-method -> ResubstituteParams-class.html [ SUCCESS ]
    SVMinterface                            html  
REDIRECT:topic	 SVMtrainInterface -> SVMinterface.html [ SUCCESS ]
REDIRECT:topic	 SVMtrainInterface,matrix-method -> SVMinterface.html [ SUCCESS ]
REDIRECT:topic	 SVMtrainInterface,DataFrame-method -> SVMinterface.html [ SUCCESS ]
REDIRECT:topic	 SVMtrainInterface,MultiAssayExperiment-method -> SVMinterface.html [ SUCCESS ]
REDIRECT:topic	 SVMpredictInterface -> SVMinterface.html [ SUCCESS ]
REDIRECT:topic	 SVMpredictInterface,svm,matrix-method -> SVMinterface.html [ SUCCESS ]
REDIRECT:topic	 SVMpredictInterface,svm,DataFrame-method -> SVMinterface.html [ SUCCESS ]
REDIRECT:topic	 SVMpredictInterface,svm,MultiAssayExperiment-method -> SVMinterface.html [ SUCCESS ]
REDIRECT:file	 SVMinterface.html -> SVMinterface.html [ SUCCESS ]
    SelectParams-class                      html  
REDIRECT:topic	 SelectParams -> SelectParams-class.html [ SUCCESS ]
REDIRECT:topic	 SelectParams-class -> SelectParams-class.html [ SUCCESS ]
REDIRECT:topic	 SelectParams,ANY-method -> SelectParams-class.html [ SUCCESS ]
REDIRECT:topic	 SelectParams,functionOrList-method -> SelectParams-class.html [ SUCCESS ]
    SelectResult-class                      html  
REDIRECT:topic	 SelectResult -> SelectResult-class.html [ SUCCESS ]
REDIRECT:topic	 SelectResult-class -> SelectResult-class.html [ SUCCESS ]
REDIRECT:topic	 SelectResult,character,character,numeric,list,list-method -> SelectResult-class.html [ SUCCESS ]
REDIRECT:topic	 show,SelectResult-method -> SelectResult-class.html [ SUCCESS ]
    TrainParams-class                       html  
REDIRECT:topic	 TrainParams -> TrainParams-class.html [ SUCCESS ]
REDIRECT:topic	 TrainParams-class -> TrainParams-class.html [ SUCCESS ]
REDIRECT:topic	 TrainParams,ANY-method -> TrainParams-class.html [ SUCCESS ]
REDIRECT:topic	 TrainParams,function-method -> TrainParams-class.html [ SUCCESS ]
    TransformParams-class                   html  
REDIRECT:topic	 TransformParams -> TransformParams-class.html [ SUCCESS ]
REDIRECT:topic	 TransformParams-class -> TransformParams-class.html [ SUCCESS ]
REDIRECT:topic	 TransformParams,ANY-method -> TransformParams-class.html [ SUCCESS ]
REDIRECT:topic	 TransformParams,function-method -> TransformParams-class.html [ SUCCESS ]
    asthmaDataset                           html  
REDIRECT:topic	 measurements -> asthmaDataset.html [ SUCCESS ]
REDIRECT:topic	 classes -> asthmaDataset.html [ SUCCESS ]
REDIRECT:file	 asthmaDataset.html -> asthmaDataset.html [ SUCCESS ]
    bartlettSelection                       html  
REDIRECT:topic	 bartlettSelection -> bartlettSelection.html [ SUCCESS ]
REDIRECT:topic	 bartlettSelection,matrix-method -> bartlettSelection.html [ SUCCESS ]
REDIRECT:topic	 bartlettSelection,DataFrame-method -> bartlettSelection.html [ SUCCESS ]
REDIRECT:topic	 bartlettSelection,MultiAssayExperiment-method -> bartlettSelection.html [ SUCCESS ]
    calcPerformance                         html  
REDIRECT:topic	 calcPerformance -> calcPerformance.html [ SUCCESS ]
REDIRECT:topic	 calcExternalPerformance -> calcPerformance.html [ SUCCESS ]
REDIRECT:topic	 calcCVperformance -> calcPerformance.html [ SUCCESS ]
REDIRECT:topic	 calcExternalPerformance,factor,factor-method -> calcPerformance.html [ SUCCESS ]
REDIRECT:topic	 calcCVperformance,ClassifyResult-method -> calcPerformance.html [ SUCCESS ]
    characterOrDataFrame-class              html  
REDIRECT:topic	 characterOrDataFrame -> characterOrDataFrame-class.html [ SUCCESS ]
REDIRECT:topic	 characterOrDataFrame-class -> characterOrDataFrame-class.html [ SUCCESS ]
    classifyInterface                       html  
REDIRECT:topic	 classifyInterface -> classifyInterface.html [ SUCCESS ]
REDIRECT:topic	 classifyInterface,matrix-method -> classifyInterface.html [ SUCCESS ]
REDIRECT:topic	 classifyInterface,DataFrame-method -> classifyInterface.html [ SUCCESS ]
REDIRECT:topic	 classifyInterface,MultiAssayExperiment-method -> classifyInterface.html [ SUCCESS ]
    differentMeansSelection                 html  
REDIRECT:topic	 differentMeansSelection -> differentMeansSelection.html [ SUCCESS ]
REDIRECT:topic	 differentMeansSelection,matrix-method -> differentMeansSelection.html [ SUCCESS ]
REDIRECT:topic	 differentMeansSelection,DataFrame-method -> differentMeansSelection.html [ SUCCESS ]
REDIRECT:topic	 differentMeansSelection,MultiAssayExperiment-method -> differentMeansSelection.html [ SUCCESS ]
    distribution                            html  
REDIRECT:topic	 distribution -> distribution.html [ SUCCESS ]
REDIRECT:topic	 distribution,ClassifyResult-method -> distribution.html [ SUCCESS ]
    dlda-class                              html  
REDIRECT:topic	 dlda -> dlda-class.html [ SUCCESS ]
REDIRECT:topic	 dlda-class -> dlda-class.html [ SUCCESS ]
    easyHardClassifier                      html  
REDIRECT:topic	 easyHardClassifier -> easyHardClassifier.html [ SUCCESS ]
REDIRECT:topic	 easyHardClassifierTrain -> easyHardClassifier.html [ SUCCESS ]
REDIRECT:topic	 easyHardClassifierTrain,MultiAssayExperiment-method -> easyHardClassifier.html [ SUCCESS ]
REDIRECT:topic	 easyHardClassifierPredict -> easyHardClassifier.html [ SUCCESS ]
REDIRECT:topic	 easyHardClassifierPredict,EasyHardClassifier,MultiAssayExperiment-method -> easyHardClassifier.html [ SUCCESS ]
Rd warning: Previous alias or file overwritten by alias: easyHardClassifier
    easyHardFeatures                        html  
REDIRECT:topic	 easyHardFeatures -> easyHardFeatures.html [ SUCCESS ]
REDIRECT:topic	 easyHardFeatures,EasyHardClassifier-method -> easyHardFeatures.html [ SUCCESS ]
    edgeRselection                          html  
REDIRECT:topic	 edgeRselection -> edgeRselection.html [ SUCCESS ]
REDIRECT:topic	 edgeRselection,matrix-method -> edgeRselection.html [ SUCCESS ]
REDIRECT:topic	 edgeRselection,DataFrame-method -> edgeRselection.html [ SUCCESS ]
REDIRECT:topic	 edgeRselection,MultiAssayExperiment-method -> edgeRselection.html [ SUCCESS ]
    edgesToHubNetworks                      html  
REDIRECT:topic	 edgesToHubNetworks -> edgesToHubNetworks.html [ SUCCESS ]
    elasticNetFeatures                      html  
REDIRECT:topic	 elasticNetFeatures -> elasticNetFeatures.html [ SUCCESS ]
REDIRECT:topic	 elasticNetFeatures,multnet-method -> elasticNetFeatures.html [ SUCCESS ]
    elasticNetGLMinterface                  html  
REDIRECT:topic	 elasticNetGLMinterface -> elasticNetGLMinterface.html [ SUCCESS ]
REDIRECT:topic	 elasticNetGLMtrainInterface -> elasticNetGLMinterface.html [ SUCCESS ]
REDIRECT:topic	 elasticNetGLMpredictInterface -> elasticNetGLMinterface.html [ SUCCESS ]
REDIRECT:topic	 elasticNetGLMtrainInterface,matrix-method -> elasticNetGLMinterface.html [ SUCCESS ]
REDIRECT:topic	 elasticNetGLMtrainInterface,DataFrame-method -> elasticNetGLMinterface.html [ SUCCESS ]
REDIRECT:topic	 elasticNetGLMtrainInterface,MultiAssayExperiment-method -> elasticNetGLMinterface.html [ SUCCESS ]
REDIRECT:topic	 elasticNetGLMpredictInterface,multnet,matrix-method -> elasticNetGLMinterface.html [ SUCCESS ]
REDIRECT:topic	 elasticNetGLMpredictInterface,multnet,DataFrame-method -> elasticNetGLMinterface.html [ SUCCESS ]
REDIRECT:topic	 elasticNetGLMpredictInterface,multnet,MultiAssayExperiment-method -> elasticNetGLMinterface.html [ SUCCESS ]
    featureSetSummary                       html  
REDIRECT:topic	 featureSetSummary -> featureSetSummary.html [ SUCCESS ]
REDIRECT:topic	 featureSetSummary,matrix-method -> featureSetSummary.html [ SUCCESS ]
REDIRECT:topic	 featureSetSummary,DataFrame-method -> featureSetSummary.html [ SUCCESS ]
REDIRECT:topic	 featureSetSummary,MultiAssayExperiment-method -> featureSetSummary.html [ SUCCESS ]
    fisherDiscriminant                      html  
REDIRECT:topic	 fisherDiscriminant -> fisherDiscriminant.html [ SUCCESS ]
REDIRECT:topic	 fisherDiscriminant,matrix-method -> fisherDiscriminant.html [ SUCCESS ]
REDIRECT:topic	 fisherDiscriminant,DataFrame-method -> fisherDiscriminant.html [ SUCCESS ]
REDIRECT:topic	 fisherDiscriminant,MultiAssayExperiment-method -> fisherDiscriminant.html [ SUCCESS ]
    forestFeatures                          html  
REDIRECT:topic	 forestFeatures -> forestFeatures.html [ SUCCESS ]
REDIRECT:topic	 forestFeatures,randomForest-method -> forestFeatures.html [ SUCCESS ]
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** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'ClassifyR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ClassifyR' as ClassifyR_2.11.0.zip
* DONE (ClassifyR)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'ClassifyR' successfully unpacked and MD5 sums checked

Tests output


Example timings

ClassifyR.Rcheck/examples_i386/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 5.87 0.1239.52
DLDAinterface0.050.000.04
DMDselection3.010.023.03
EasyHardClassifier-class0.020.000.02
FeatureSetCollection-class0.010.000.02
FeatureSetCollectionOrNULL-class000
KolmogorovSmirnovSelection1.110.061.17
KullbackLeiblerSelection0.610.000.61
MixModelsListsSet-class0.190.000.27
NSCpredictInterface0.080.000.08
NSCselectionInterface0.10.00.1
NSCtrainInterface0.030.000.03
PredictParams-class000
ROCplot0.360.000.38
ResubstituteParams-class000
SVMinterface0.040.000.04
SelectParams-class0.010.000.01
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection1.160.011.17
calcPerformance000
characterOrDataFrame-class000
classifyInterface0.510.040.58
differentMeansSelection0.880.040.92
distribution 1.08 0.1324.53
easyHardClassifier0.180.010.21
easyHardFeatures0.180.000.17
edgeRselection2.650.022.67
edgesToHubNetworks000
elasticNetFeatures 0.67 0.0014.03
elasticNetGLMinterface 0.50 0.0113.73
featureSetSummary000
fisherDiscriminant0.030.000.03
forestFeatures0.060.000.07
functionOrList-class000
functionOrNULL-class000
getLocationsAndScales0.020.000.02
integerOrNumeric-class0.010.000.01
interactorDifferences0.020.000.02
kTSPclassifier0.030.000.03
knnInterface0.010.000.02
leveneSelection0.670.020.69
likelihoodRatioSelection2.710.002.70
limmaSelection0.180.000.19
listOrCharacterOrNULL-class0.020.000.01
listOrNULL-class000
mixmodels0.130.000.13
naiveBayesKernel0.250.000.25
networkCorrelationsSelection0.100.000.11
pairsDifferencesSelection0.150.000.14
performancePlot0.210.000.23
plotFeatureClasses1.220.001.22
previousSelection 1.05 0.0219.62
previousTrained 0.98 0.0320.78
randomForestInterface0.170.000.17
rankingPlot1.360.037.50
runTest2.270.112.38
runTests 2.04 0.2538.36
samplesMetricMap1.490.001.48
selectionPlot1.650.007.61
subtractFromLocation000

ClassifyR.Rcheck/examples_x64/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 6.86 0.2747.05
DLDAinterface0.050.000.05
DMDselection3.240.123.36
EasyHardClassifier-class0.010.000.02
FeatureSetCollection-class0.020.000.01
FeatureSetCollectionOrNULL-class000
KolmogorovSmirnovSelection1.300.101.39
KullbackLeiblerSelection0.610.000.61
MixModelsListsSet-class0.200.000.25
NSCpredictInterface0.090.000.10
NSCselectionInterface0.050.010.06
NSCtrainInterface0.050.000.05
PredictParams-class000
ROCplot0.420.000.44
ResubstituteParams-class000
SVMinterface0.050.000.04
SelectParams-class000
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection1.170.001.18
calcPerformance0.010.000.01
characterOrDataFrame-class000
classifyInterface0.860.060.92
differentMeansSelection1.160.051.20
distribution 1.45 0.1527.57
easyHardClassifier0.360.000.36
easyHardFeatures0.310.000.31
edgeRselection3.920.144.07
edgesToHubNetworks000
elasticNetFeatures 1.00 0.0021.66
elasticNetGLMinterface 0.78 0.0419.33
featureSetSummary000
fisherDiscriminant0.050.000.04
forestFeatures0.080.000.08
functionOrList-class000
functionOrNULL-class0.010.000.01
getLocationsAndScales0.040.000.03
integerOrNumeric-class0.010.000.02
interactorDifferences0.030.000.03
kTSPclassifier0.060.000.06
knnInterface0.040.000.04
leveneSelection0.710.020.73
likelihoodRatioSelection4.100.004.09
limmaSelection0.220.000.22
listOrCharacterOrNULL-class000
listOrNULL-class000
mixmodels0.190.000.19
naiveBayesKernel0.410.000.40
networkCorrelationsSelection0.170.000.17
pairsDifferencesSelection0.250.000.25
performancePlot0.410.000.40
plotFeatureClasses1.520.001.53
previousSelection 1.40 0.0122.61
previousTrained 1.28 0.0021.54
randomForestInterface0.110.000.11
rankingPlot1.350.007.36
runTest3.360.023.37
runTests 2.17 0.1740.82
samplesMetricMap2.400.002.41
selectionPlot1.880.008.66
subtractFromLocation0.010.000.01