Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:20 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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? 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: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 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 -0400 (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: 2022-04-12 17:21:14 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:38:25 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 1031.3 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 4.1.3 (2022-03-10)
* 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           7.21   0.37    7.58
ROCplot                5.52   0.33    5.85
runTests               3.75   0.34   57.37
distribution           2.43   0.80   37.11
selectionPlot          2.93   0.01   21.00
rankingPlot            2.64   0.05   20.58
ClassifyResult-class   1.99   0.61   51.12
plotFeatureClasses     2.19   0.00    7.26
previousTrained        1.84   0.06   41.94
previousSelection      1.78   0.02   42.88
elasticNetFeatures     1.23   0.03   32.83
elasticNetGLMinterface 1.15   0.02   35.49
mixmodels              0.33   0.00   13.85
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
DMDselection             8.77   0.02    8.78
ROCplot                  5.30   0.06    5.36
likelihoodRatioSelection 5.03   0.00    5.03
runTests                 3.64   0.53   55.69
selectionPlot            3.70   0.05   22.43
rankingPlot              3.18   0.02   22.34
distribution             2.22   0.39   41.98
ClassifyResult-class     1.82   0.61   50.42
previousTrained          2.04   0.10   42.11
previousSelection        2.05   0.02   43.00
elasticNetFeatures       1.52   0.04   32.91
elasticNetGLMinterface   1.28   0.05   36.22
* 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
  4 1011k    4 44360    0     0   278k      0  0:00:03 --:--:--  0:00:03  279k
100 1011k  100 1011k    0     0   946k      0  0:00:01  0:00:01 --:--:--  948k

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 1.99 0.6151.12
DLDAinterface0.110.000.11
DMDselection7.210.377.58
EasyHardClassifier-class0.010.000.01
FeatureSetCollection-class000
FeatureSetCollectionOrNULL-class000
KolmogorovSmirnovSelection2.550.082.63
KullbackLeiblerSelection1.510.001.51
MixModelsListsSet-class0.440.051.07
NSCpredictInterface0.160.010.17
NSCselectionInterface0.10.00.1
NSCtrainInterface0.080.000.08
PredictParams-class000
ROCplot5.520.335.85
ResubstituteParams-class0.010.000.01
SVMinterface0.080.060.14
SelectParams-class0.020.000.01
SelectResult-class000
TrainParams-class000
TransformParams-class0.010.000.02
bartlettSelection2.690.593.28
calcPerformance000
characterOrDataFrame-class0.010.000.02
classifyInterface1.660.101.75
differentMeansSelection1.630.652.28
distribution 2.43 0.8037.11
easyHardClassifier0.470.000.46
easyHardFeatures0.330.000.33
edgeRselection4.540.034.62
edgesToHubNetworks000
elasticNetFeatures 1.23 0.0332.83
elasticNetGLMinterface 1.15 0.0235.49
featureSetSummary000
fisherDiscriminant0.100.000.09
forestFeatures0.140.000.14
functionOrList-class000
functionOrNULL-class0.010.000.02
getLocationsAndScales0.020.000.01
integerOrNumeric-class0.020.000.02
interactorDifferences0.060.000.06
kTSPclassifier0.090.000.09
knnInterface0.030.010.05
leveneSelection0.910.000.91
likelihoodRatioSelection4.640.004.64
limmaSelection0.330.000.33
listOrCharacterOrNULL-class000
listOrNULL-class0.010.000.01
mixmodels 0.33 0.0013.85
naiveBayesKernel0.550.000.54
networkCorrelationsSelection0.220.000.22
pairsDifferencesSelection0.220.000.22
performancePlot0.370.000.38
plotFeatureClasses2.190.007.26
previousSelection 1.78 0.0242.88
previousTrained 1.84 0.0641.94
randomForestInterface0.250.000.25
rankingPlot 2.64 0.0520.58
runTest3.250.083.33
runTests 3.75 0.3457.37
samplesMetricMap2.410.002.42
selectionPlot 2.93 0.0121.00
subtractFromLocation000

ClassifyR.Rcheck/examples_x64/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 1.82 0.6150.42
DLDAinterface0.110.000.11
DMDselection8.770.028.78
EasyHardClassifier-class0.030.000.03
FeatureSetCollection-class000
FeatureSetCollectionOrNULL-class000
KolmogorovSmirnovSelection3.610.143.75
KullbackLeiblerSelection0.940.000.93
MixModelsListsSet-class0.620.020.91
NSCpredictInterface0.210.000.20
NSCselectionInterface0.140.000.14
NSCtrainInterface0.130.000.12
PredictParams-class000
ROCplot5.300.065.36
ResubstituteParams-class000
SVMinterface0.080.000.08
SelectParams-class0.010.000.01
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection3.690.003.69
calcPerformance0.020.000.02
characterOrDataFrame-class0.010.000.01
classifyInterface1.320.051.36
differentMeansSelection2.920.032.95
distribution 2.22 0.3941.98
easyHardClassifier0.520.000.52
easyHardFeatures0.470.000.47
edgeRselection4.140.054.19
edgesToHubNetworks000
elasticNetFeatures 1.52 0.0432.91
elasticNetGLMinterface 1.28 0.0536.22
featureSetSummary000
fisherDiscriminant0.130.000.13
forestFeatures0.170.000.17
functionOrList-class000
functionOrNULL-class0.020.000.02
getLocationsAndScales0.030.000.03
integerOrNumeric-class0.010.000.01
interactorDifferences0.050.000.05
kTSPclassifier0.110.000.11
knnInterface0.050.000.05
leveneSelection1.010.001.01
likelihoodRatioSelection5.030.005.03
limmaSelection0.440.000.44
listOrCharacterOrNULL-class000
listOrNULL-class000
mixmodels0.240.000.27
naiveBayesKernel0.570.000.57
networkCorrelationsSelection0.320.000.32
pairsDifferencesSelection0.260.000.26
performancePlot0.50.00.5
plotFeatureClasses2.080.002.08
previousSelection 2.05 0.0243.00
previousTrained 2.04 0.1042.11
randomForestInterface0.370.000.38
rankingPlot 3.18 0.0222.34
runTest3.720.033.75
runTests 3.64 0.5355.69
samplesMetricMap3.060.003.06
selectionPlot 3.70 0.0522.43
subtractFromLocation000