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CHECK report for ClassifyR on tokay2

This page was generated on 2019-10-16 12:30:44 -0400 (Wed, 16 Oct 2019).

Package 280/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.4.4
Dario Strbenac
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: RELEASE_3_9
Last Commit: a2993e1
Last Changed Date: 2019-06-14 02:44:32 -0400 (Fri, 14 Jun 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 2.4.4
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ClassifyR_2.4.4.tar.gz
StartedAt: 2019-10-16 02:41:35 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:55:06 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 811.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ClassifyR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ClassifyR_2.4.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '2.4.4'
* 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: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi6IFSc/R.INSTALL23244fd146f9/ClassifyR/man/differentMeansSelection.Rd:40: file link 'rowttests' in package 'genefilter' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi6IFSc/R.INSTALL23244fd146f9/ClassifyR/man/distribution.Rd:32: file link 'stat_density' in package 'ggplot2' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi6IFSc/R.INSTALL23244fd146f9/ClassifyR/man/edgeRselection.Rd:45: file link 'edgeR' in package 'edgeR' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-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 : : no visible global function definition
  for 'dmvnorm'
kTSPclassifier,DataFrame : : no visible global function
  definition for 'Pairs'
plotFeatureClasses,DataFrame : : no visible binding for
  global variable 'measurement'
plotFeatureClasses,DataFrame : : no visible binding for
  global variable '..density..'
plotFeatureClasses,DataFrame : : no visible binding for
  global variable 'legends grouping'
plotFeatureClasses,DataFrame : : no visible binding for
  global variable 'key'
plotFeatureClasses,DataFrame : : no visible binding for
  global variable 'value'
plotFeatureClasses,DataFrame : : no visible binding for
  global variable 'ID'
rankingPlot,list :  : : no visible global
  function definition for 'first'
rankingPlot,list :  : : no visible global
  function definition for 'second'
rankingPlot,list :  :  : : no visible
  global function definition for 'first'
rankingPlot,list :  :  : : no visible
  global function definition for 'second'
runTest,DataFrame: no visible binding for global variable 'setsNodes'
runTests,DataFrame: no visible binding for global variable 'setsNodes'
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 :  : : no visible global
  function definition for 'first'
selectionPlot,list :  : : no visible global
  function definition for 'second'
selectionPlot,list :  :  : : no
  visible global function definition for 'first'
selectionPlot,list :  :  : : no
  visible global function definition for 'second'
selectionPlot,list: no visible binding for global variable 'Freq'
Undefined global functions or variables:
  ..density.. 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 or elapsed time > 5s
                         user system elapsed
likelihoodRatioSelection 6.99   0.37    7.36
DMDselection             6.25   0.26    6.52
edgeRselection           6.06   0.20    6.26
selectionPlot            2.86   0.00   13.84
ClassifyResult-class     2.22   0.35   49.59
distribution             2.22   0.17   33.99
rankingPlot              2.02   0.06   10.65
previousSelection        1.72   0.00   24.20
previousTrained          1.48   0.05   25.24
runTests                 1.16   0.15   37.28
elasticNetGLMinterface   0.92   0.03   25.97
elasticNetFeatures       0.88   0.02   25.72
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
likelihoodRatioSelection 5.92   0.03    5.95
DMDselection             5.67   0.02    5.69
edgeRselection           4.93   0.08    5.00
selectionPlot            3.25   0.02   12.14
ClassifyResult-class     2.84   0.28   59.84
rankingPlot              2.98   0.05   12.50
previousTrained          1.92   0.00   25.21
distribution             1.48   0.23   37.02
previousSelection        1.63   0.01   28.07
runTests                 1.19   0.18   39.42
elasticNetGLMinterface   1.03   0.03   26.47
elasticNetFeatures       0.89   0.00   22.64
* 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
  'C:/Users/biocbuild/bbs-3.9-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 https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ClassifyR_2.4.4.tar.gz && rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ClassifyR.buildbin-libdir ClassifyR_2.4.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ClassifyR_2.4.4.zip && rm ClassifyR_2.4.4.tar.gz ClassifyR_2.4.4.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  993k  100  993k    0     0  15.0M      0 --:--:-- --:--:-- --:--:-- 16.7M

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  
    finding level-2 HTML links ... done

    DLDAinterface                           html  
    DMDselection                            html  
    FeatureSetCollection-class              html  
    FeatureSetCollectionOrNULL-class        html  
    KolmogorovSmirnovSelection              html  
    KullbackLeiblerSelection                html  
    MixModelsListsSet-class                 html  
    NSCpredictInterface                     html  
    NSCselectionInterface                   html  
    NSCtrainInterface                       html  
    PredictParams-class                     html  
    ROCplot                                 html  
    ResubstituteParams-class                html  
    SVMinterface                            html  
    SelectParams-class                      html  
    SelectResult-class                      html  
    TrainParams-class                       html  
    TransformParams-class                   html  
    asthmaDataset                           html  
    bartlettSelection                       html  
    calcPerformance                         html  
    characterOrDataFrame-class              html  
    classifyInterface                       html  
    differentMeansSelection                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi6IFSc/R.INSTALL23244fd146f9/ClassifyR/man/differentMeansSelection.Rd:40: file link 'rowttests' in package 'genefilter' does not exist and so has been treated as a topic
    distribution                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi6IFSc/R.INSTALL23244fd146f9/ClassifyR/man/distribution.Rd:32: file link 'stat_density' in package 'ggplot2' does not exist and so has been treated as a topic
    dlda-class                              html  
    edgeRselection                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpi6IFSc/R.INSTALL23244fd146f9/ClassifyR/man/edgeRselection.Rd:45: file link 'edgeR' in package 'edgeR' does not exist and so has been treated as a topic
    edgesToHubNetworks                      html  
    elasticNetFeatures                      html  
    elasticNetGLMinterface                  html  
    featureSetSummary                       html  
    fisherDiscriminant                      html  
    forestFeatures                          html  
    functionOrList-class                    html  
    functionOrNULL-class                    html  
    getLocationsAndScales                   html  
    integerOrNumeric-class                  html  
    interactorDifferences                   html  
    kTSPclassifier                          html  
    knnInterface                            html  
    leveneSelection                         html  
    likelihoodRatioSelection                html  
    limmaSelection                          html  
    mixmodels                               html  
    multnet-class                           html  
    naiveBayesKernel                        html  
    networkCorrelationsSelection            html  
    pairsDifferencesSelection               html  
    pamrtrained-class                       html  
    performancePlot                         html  
    plotFeatureClasses                      html  
    previousSelection                       html  
    previousTrained                         html  
    randomForest-class                      html  
    randomForestInterface                   html  
    rankingPlot                             html  
    runTest                                 html  
    runTests                                html  
    samplesMetricMap                        html  
    selectionPlot                           html  
    subtractFromLocation                    html  
    svm-class                               html  
** 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_2.4.4.zip
* DONE (ClassifyR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-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 2.22 0.3549.59
DLDAinterface0.080.000.08
DMDselection6.250.266.52
FeatureSetCollection-class0.010.000.02
FeatureSetCollectionOrNULL-class000
KolmogorovSmirnovSelection2.740.062.79
KullbackLeiblerSelection1.400.081.49
MixModelsListsSet-class0.500.000.84
NSCpredictInterface0.160.030.19
NSCselectionInterface0.090.020.11
NSCtrainInterface0.080.020.09
PredictParams-class000
ROCplot101
ResubstituteParams-class000
SVMinterface0.080.000.08
SelectParams-class0.010.000.01
SelectResult-class000
TrainParams-class0.020.000.02
TransformParams-class000
bartlettSelection2.200.042.25
calcPerformance000
characterOrDataFrame-class0.020.000.01
classifyInterface1.290.161.50
differentMeansSelection1.390.031.42
distribution 2.22 0.1733.99
edgeRselection6.060.206.26
edgesToHubNetworks000
elasticNetFeatures 0.88 0.0225.72
elasticNetGLMinterface 0.92 0.0325.97
featureSetSummary000
fisherDiscriminant0.090.000.10
forestFeatures0.160.000.15
functionOrList-class000
functionOrNULL-class0.010.000.01
getLocationsAndScales0.030.000.03
integerOrNumeric-class0.020.000.02
interactorDifferences0.060.000.06
kTSPclassifier0.110.000.11
knnInterface0.050.000.05
leveneSelection1.510.331.84
likelihoodRatioSelection6.990.377.36
limmaSelection0.50.00.5
mixmodels0.330.000.35
naiveBayesKernel0.680.000.68
networkCorrelationsSelection0.250.000.25
pairsDifferencesSelection0.330.000.33
performancePlot0.310.000.31
plotFeatureClasses3.30.03.3
previousSelection 1.72 0.0024.20
previousTrained 1.48 0.0525.24
randomForestInterface0.220.000.22
rankingPlot 2.02 0.0610.65
runTest0.560.040.60
runTests 1.16 0.1537.28
samplesMetricMap4.310.004.31
selectionPlot 2.86 0.0013.84
subtractFromLocation000

ClassifyR.Rcheck/examples_x64/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 2.84 0.2859.84
DLDAinterface0.080.000.07
DMDselection5.670.025.69
FeatureSetCollection-class000
FeatureSetCollectionOrNULL-class000
KolmogorovSmirnovSelection1.870.011.89
KullbackLeiblerSelection0.940.000.94
MixModelsListsSet-class0.390.000.41
NSCpredictInterface0.110.020.12
NSCselectionInterface0.090.020.11
NSCtrainInterface0.080.000.08
PredictParams-class000
ROCplot0.750.000.75
ResubstituteParams-class0.020.000.02
SVMinterface0.040.000.04
SelectParams-class0.020.000.02
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection1.330.001.33
calcPerformance0.010.000.01
characterOrDataFrame-class000
classifyInterface1.890.112.00
differentMeansSelection1.190.031.22
distribution 1.48 0.2337.02
edgeRselection4.930.085.00
edgesToHubNetworks000
elasticNetFeatures 0.89 0.0022.64
elasticNetGLMinterface 1.03 0.0326.47
featureSetSummary0.010.000.01
fisherDiscriminant0.100.000.09
forestFeatures0.170.000.18
functionOrList-class0.020.000.01
functionOrNULL-class000
getLocationsAndScales0.040.000.05
integerOrNumeric-class0.020.000.01
interactorDifferences0.060.000.07
kTSPclassifier0.130.000.12
knnInterface0.040.000.05
leveneSelection1.710.021.72
likelihoodRatioSelection5.920.035.95
limmaSelection0.580.000.58
mixmodels0.370.000.48
naiveBayesKernel0.580.000.58
networkCorrelationsSelection0.150.000.16
pairsDifferencesSelection0.220.000.22
performancePlot0.240.000.23
plotFeatureClasses2.510.002.52
previousSelection 1.63 0.0128.07
previousTrained 1.92 0.0025.21
randomForestInterface0.250.000.25
rankingPlot 2.98 0.0512.50
runTest0.830.050.87
runTests 1.19 0.1839.42
samplesMetricMap4.140.004.15
selectionPlot 3.25 0.0212.14
subtractFromLocation000