Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:06:07 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ClassifyR on tokay2


To the developers/maintainers of the ClassifyR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClassifyR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 324/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.14.0  (landing page)
Dario Strbenac
Snapshot Date: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 2022)
git_url: https://git.bioconductor.org/packages/ClassifyR
git_branch: RELEASE_3_14
git_last_commit: 133d20a
git_last_commit_date: 2021-10-26 12:15:09 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ClassifyR
Version: 2.14.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ClassifyR_2.14.0.tar.gz
StartedAt: 2022-01-20 17:34:27 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 17:51:04 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 997.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ClassifyR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ClassifyR_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ClassifyR.Rcheck'
* using R version 4.1.2 (2021-11-01)
* 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 '2.14.0'
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'MultiAssayExperiment'
A package should be listed in only one of these fields.
* 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 global function definition for 'mcols'
runTests,DataFrame: no visible binding for global variable 'setsNodes'
runTests,DataFrame: no visible binding for global variable 'dataset'
runTests,DataFrame : <anonymous>: no visible global function definition
  for 'mcols'
runTests,DataFrame : <anonymous>: no visible global function definition
  for 'mcols<-'
runTests,DataFrame: no visible global function definition for 'mcols<-'
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 dataset
  dmvnorm first key legends grouping mcols mcols<- 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
DMDselection           6.75   0.52    7.27
runTests               3.45   0.57   53.60
distribution           2.33   0.63   40.37
selectionPlot          2.92   0.03   20.33
rankingPlot            2.81   0.01   21.20
ClassifyResult-class   1.86   0.49   55.52
previousTrained        1.67   0.00   37.11
previousSelection      1.56   0.07   39.67
elasticNetFeatures     1.33   0.01   34.73
elasticNetGLMinterface 0.92   0.07   32.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
DMDselection           6.53   0.16    6.69
runTests               2.94   0.50   56.00
selectionPlot          3.22   0.09   22.43
rankingPlot            3.17   0.03   22.59
distribution           1.91   0.45   36.61
ClassifyResult-class   1.66   0.53   54.06
previousTrained        1.94   0.05   41.16
previousSelection      1.78   0.08   40.31
elasticNetFeatures     1.08   0.04   34.85
elasticNetGLMinterface 1.08   0.02   42.95
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.



Installation output

ClassifyR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ClassifyR_2.14.0.tar.gz && rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ClassifyR.buildbin-libdir ClassifyR_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ClassifyR_2.14.0.zip && rm ClassifyR_2.14.0.tar.gz ClassifyR_2.14.0.zip
###
##############################################################################
##############################################################################


  % 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 1011k  100 1011k    0     0  1834k      0 --:--:-- --:--:-- --:--:-- 1839k

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  
    EasyHardClassifier-class                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  
    distribution                            html  
    dlda-class                              html  
    easyHardClassifier                      html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/ClassifyR.buildbin-libdir/00LOCK-ClassifyR/00new/ClassifyR/help/easyHardClassifier.html
    easyHardFeatures                        html  
    edgeRselection                          html  
    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  
    listOrCharacterOrNULL-class             html  
    listOrNULL-class                        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_2.14.0.zip
* DONE (ClassifyR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-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 1.86 0.4955.52
DLDAinterface0.140.000.14
DMDselection6.750.527.27
EasyHardClassifier-class0.020.000.01
FeatureSetCollection-class000
FeatureSetCollectionOrNULL-class000
KolmogorovSmirnovSelection2.090.082.17
KullbackLeiblerSelection1.630.011.65
MixModelsListsSet-class0.430.021.53
NSCpredictInterface0.060.080.14
NSCselectionInterface0.110.010.13
NSCtrainInterface0.080.000.08
PredictParams-class0.020.000.01
ROCplot4.700.284.99
ResubstituteParams-class000
SVMinterface0.060.050.11
SelectParams-class0.020.000.01
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection1.980.382.36
calcPerformance0.020.000.02
characterOrDataFrame-class0.000.010.01
classifyInterface1.360.141.50
differentMeansSelection1.390.391.78
distribution 2.33 0.6340.37
easyHardClassifier0.490.010.50
easyHardFeatures0.340.000.35
edgeRselection3.840.023.95
edgesToHubNetworks000
elasticNetFeatures 1.33 0.0134.73
elasticNetGLMinterface 0.92 0.0732.11
featureSetSummary000
fisherDiscriminant0.110.000.11
forestFeatures0.170.000.18
functionOrList-class000
functionOrNULL-class0.020.000.01
getLocationsAndScales0.030.000.03
integerOrNumeric-class0.020.000.02
interactorDifferences0.030.010.04
kTSPclassifier0.110.000.11
knnInterface0.030.000.04
leveneSelection0.920.020.93
likelihoodRatioSelection404
limmaSelection0.310.000.32
listOrCharacterOrNULL-class000
listOrNULL-class000
mixmodels0.210.000.21
naiveBayesKernel0.450.000.46
networkCorrelationsSelection0.190.000.18
pairsDifferencesSelection0.220.000.22
performancePlot0.320.000.33
plotFeatureClasses1.600.011.61
previousSelection 1.56 0.0739.67
previousTrained 1.67 0.0037.11
randomForestInterface0.30.00.3
rankingPlot 2.81 0.0121.20
runTest3.330.063.39
runTests 3.45 0.5753.60
samplesMetricMap2.220.012.26
selectionPlot 2.92 0.0320.33
subtractFromLocation000

ClassifyR.Rcheck/examples_x64/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 1.66 0.5354.06
DLDAinterface0.090.000.10
DMDselection6.530.166.69
EasyHardClassifier-class0.010.000.01
FeatureSetCollection-class0.020.000.02
FeatureSetCollectionOrNULL-class000
KolmogorovSmirnovSelection2.060.062.12
KullbackLeiblerSelection1.660.021.68
MixModelsListsSet-class0.580.000.86
NSCpredictInterface0.180.030.21
NSCselectionInterface0.110.000.11
NSCtrainInterface0.10.00.1
PredictParams-class000
ROCplot4.310.034.34
ResubstituteParams-class000
SVMinterface0.060.010.08
SelectParams-class000
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection2.550.052.59
calcPerformance000
characterOrDataFrame-class0.010.000.02
classifyInterface0.890.060.95
differentMeansSelection1.390.071.46
distribution 1.91 0.4536.61
easyHardClassifier0.430.010.45
easyHardFeatures0.490.000.49
edgeRselection3.640.103.73
edgesToHubNetworks000
elasticNetFeatures 1.08 0.0434.85
elasticNetGLMinterface 1.08 0.0242.95
featureSetSummary000
fisherDiscriminant0.110.000.11
forestFeatures0.170.000.18
functionOrList-class0.020.000.01
functionOrNULL-class000
getLocationsAndScales0.030.000.03
integerOrNumeric-class0.010.000.02
interactorDifferences0.040.000.04
kTSPclassifier0.140.000.14
knnInterface0.040.000.05
leveneSelection1.050.001.05
likelihoodRatioSelection4.550.024.56
limmaSelection0.360.000.36
listOrCharacterOrNULL-class000
listOrNULL-class000
mixmodels0.280.001.50
naiveBayesKernel0.560.000.56
networkCorrelationsSelection0.230.000.23
pairsDifferencesSelection0.220.000.22
performancePlot0.380.000.37
plotFeatureClasses1.830.001.83
previousSelection 1.78 0.0840.31
previousTrained 1.94 0.0541.16
randomForestInterface0.280.000.28
rankingPlot 3.17 0.0322.59
runTest4.250.124.38
runTests 2.94 0.5056.00
samplesMetricMap2.560.022.57
selectionPlot 3.22 0.0922.43
subtractFromLocation000