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CHECK report for ClassifyR on tokay2

This page was generated on 2018-10-17 08:39:02 -0400 (Wed, 17 Oct 2018).

Package 250/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 2.0.10
Dario Strbenac
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: RELEASE_3_7
Last Commit: e553f79
Last Changed Date: 2018-09-03 21:30:01 -0400 (Mon, 03 Sep 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 2.0.10
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ClassifyR_2.0.10.tar.gz
StartedAt: 2018-10-17 01:08:43 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 01:19:06 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 622.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ClassifyR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ClassifyR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ClassifyR_2.0.10.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ClassifyR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '2.0.10'
* 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-3.7-bioc/tmpdir/Rtmp0yDb8o/R.INSTALL2130e72557c/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-3.7-bioc/tmpdir/Rtmp0yDb8o/R.INSTALL2130e72557c/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-3.7-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'
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'
samplesMetricMap,list: no visible binding for global variable 'Class'
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'
selectionPlot,list: no visible binding for global variable 'Freq'
Undefined global functions or variables:
  ..density.. Class Freq Metric dmvnorm legends grouping measurement
  name type
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 7.69   0.16    7.84
DMDselection             5.86   0.23    6.09
edgeRselection           5.56   0.12    5.69
selectionPlot            2.93   0.00   13.66
distribution             1.65   0.16   35.72
rankingPlot              1.65   0.02   11.75
ClassifyResult-class     0.42   0.21   33.86
runTests                 0.32   0.17   35.33
elasticNetGLMinterface   0.14   0.00   13.51
previousSelection        0.07   0.00   21.36
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
likelihoodRatioSelection 8.94   0.03    8.97
DMDselection             7.11   0.11    7.22
plotFeatureClasses       5.97   0.00    5.97
selectionPlot            3.17   0.01   12.14
distribution             1.56   0.20   38.22
rankingPlot              1.69   0.00   10.56
ClassifyResult-class     0.57   0.19   36.02
runTests                 0.32   0.19   37.71
elasticNetGLMinterface   0.11   0.03   13.52
previousSelection        0.06   0.00   19.62
* 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-3.7-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/3.7/bioc/src/contrib/ClassifyR_2.0.10.tar.gz && rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ClassifyR.buildbin-libdir ClassifyR_2.0.10.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ClassifyR_2.0.10.zip && rm ClassifyR_2.0.10.tar.gz ClassifyR_2.0.10.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  697k  100  697k    0     0  10.4M      0 --:--:-- --:--:-- --:--:-- 11.5M

install for i386

* installing *source* package 'ClassifyR' ...
** 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  
    KolmogorovSmirnovSelection              html  
    KullbackLeiblerSelection                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  
    distribution                            html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp0yDb8o/R.INSTALL2130e72557c/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-3.7-bioc/tmpdir/Rtmp0yDb8o/R.INSTALL2130e72557c/ClassifyR/man/edgeRselection.Rd:45: file link 'edgeR' in package 'edgeR' does not exist and so has been treated as a topic
    elasticNetGLMinterface                  html  
    fisherDiscriminant                      html  
    forestFeatures                          html  
    functionOrList-class                    html  
    functionOrNULL-class                    html  
    getLocationsAndScales                   html  
    leveneSelection                         html  
    likelihoodRatioSelection                html  
    limmaSelection                          html  
    logisticRegressionInterface             html  
    mixmodels                               html  
    mnlogit-class                           html  
    multnet-class                           html  
    naiveBayesKernel                        html  
    pamrtrained-class                       html  
    performancePlot                         html  
    plotFeatureClasses                      html  
    previousSelection                       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
In R CMD INSTALL

install for x64

* installing *source* package 'ClassifyR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ClassifyR' as ClassifyR_2.0.10.zip
* DONE (ClassifyR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ClassifyR' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output


Example timings

ClassifyR.Rcheck/examples_i386/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 0.42 0.2133.86
DLDAinterface0.060.000.06
DMDselection5.860.236.09
KolmogorovSmirnovSelection2.200.052.25
KullbackLeiblerSelection1.640.011.66
NSCpredictInterface0.10.00.1
NSCselectionInterface0.060.000.06
NSCtrainInterface0.080.000.08
PredictParams-class0.010.000.01
ROCplot0.60.00.6
ResubstituteParams-class0.010.000.01
SVMinterface0.070.000.06
SelectParams-class0.010.000.02
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection2.390.002.39
calcPerformance000
characterOrDataFrame-class0.020.000.02
classifyInterface1.400.191.79
distribution 1.65 0.1635.72
edgeRselection5.560.125.69
elasticNetGLMinterface 0.14 0.0013.51
fisherDiscriminant0.230.000.24
forestFeatures0.160.000.15
functionOrList-class000
functionOrNULL-class000
getLocationsAndScales0.020.000.02
leveneSelection2.060.052.11
likelihoodRatioSelection7.690.167.84
limmaSelection1.130.001.12
logisticRegressionInterface0.780.010.82
mixmodels1.140.021.43
naiveBayesKernel0.470.040.52
performancePlot0.20.00.2
plotFeatureClasses4.120.024.14
previousSelection 0.07 0.0021.36
randomForestInterface0.070.000.08
rankingPlot 1.65 0.0211.75
runTest1.530.021.54
runTests 0.32 0.1735.33
samplesMetricMap1.290.001.28
selectionPlot 2.93 0.0013.66
subtractFromLocation000

ClassifyR.Rcheck/examples_x64/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 0.57 0.1936.02
DLDAinterface0.090.000.09
DMDselection7.110.117.22
KolmogorovSmirnovSelection2.520.032.55
KullbackLeiblerSelection1.910.001.91
NSCpredictInterface0.070.010.09
NSCselectionInterface0.060.000.06
NSCtrainInterface0.050.000.05
PredictParams-class000
ROCplot0.610.000.61
ResubstituteParams-class000
SVMinterface0.050.000.04
SelectParams-class000
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection2.690.002.69
calcPerformance000
characterOrDataFrame-class0.020.000.02
classifyInterface1.100.081.19
distribution 1.56 0.2038.22
edgeRselection4.800.094.89
elasticNetGLMinterface 0.11 0.0313.52
fisherDiscriminant0.480.000.48
forestFeatures0.080.000.08
functionOrList-class0.020.000.01
functionOrNULL-class000
getLocationsAndScales0.060.000.07
leveneSelection3.700.053.75
likelihoodRatioSelection8.940.038.97
limmaSelection1.110.001.10
logisticRegressionInterface0.870.000.90
mixmodels1.350.001.71
naiveBayesKernel0.610.000.61
performancePlot0.240.000.23
plotFeatureClasses5.970.005.97
previousSelection 0.06 0.0019.62
randomForestInterface0.110.000.11
rankingPlot 1.69 0.0010.56
runTest1.170.051.22
runTests 0.32 0.1937.71
samplesMetricMap1.140.001.14
selectionPlot 3.17 0.0112.14
subtractFromLocation000