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CHECK report for ClassifyR on tokay1

This page was generated on 2018-04-12 13:24:44 -0400 (Thu, 12 Apr 2018).

Package 237/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ClassifyR 1.12.2
Dario Strbenac
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/ClassifyR
Branch: RELEASE_3_6
Last Commit: 351e75a
Last Changed Date: 2017-11-03 01:31:52 -0400 (Fri, 03 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ClassifyR
Version: 1.12.2
Command: rm -rf ClassifyR.buildbin-libdir ClassifyR.Rcheck && mkdir ClassifyR.buildbin-libdir ClassifyR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ClassifyR.buildbin-libdir ClassifyR_1.12.2.tar.gz >ClassifyR.Rcheck\00install.out 2>&1 && cp ClassifyR.Rcheck\00install.out ClassifyR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ClassifyR.buildbin-libdir --install="check:ClassifyR-install.out" --force-multiarch --no-vignettes --timings ClassifyR_1.12.2.tar.gz
StartedAt: 2018-04-11 22:56:34 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 23:02:33 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 359.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ClassifyR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf ClassifyR.buildbin-libdir ClassifyR.Rcheck && mkdir ClassifyR.buildbin-libdir ClassifyR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ClassifyR.buildbin-libdir ClassifyR_1.12.2.tar.gz >ClassifyR.Rcheck\00install.out 2>&1 && cp ClassifyR.Rcheck\00install.out ClassifyR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ClassifyR.buildbin-libdir --install="check:ClassifyR-install.out" --force-multiarch --no-vignettes --timings ClassifyR_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ClassifyR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.12.2'
* 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-3.6-bioc/tmpdir/Rtmp0wHupk/R.INSTALL221c55ee72e0/ClassifyR/man/SelectParams-class.Rd:30: missing file link 'ExpressionSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0wHupk/R.INSTALL221c55ee72e0/ClassifyR/man/TransformParams-class.Rd:22: missing file link 'ExpressionSet'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0wHupk/R.INSTALL221c55ee72e0/ClassifyR/man/distribution.Rd:32: missing file link 'stat_density'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0wHupk/R.INSTALL221c55ee72e0/ClassifyR/man/edgeRselection.Rd:40: missing file link 'edgeR'
See 'C:/Users/biocbuild/bbs-3.6-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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
.doTest : <anonymous>: no visible global function definition for
  'capture.output'
KolmogorovSmirnovSelection,ExpressionSet : <anonymous>: no visible
  global function definition for 'ks.test'
PredictParams,ANY: no visible binding for global variable 'predict'
TrainParams,ANY: no visible binding for global variable 'dlda'
bartlettSelection,ExpressionSet : <anonymous>: no visible global
  function definition for 'bartlett.test'
edgeRselection,ExpressionSet: no visible global function definition for
  'model.matrix'
fisherDiscriminant,ExpressionSet: no visible binding for global
  variable 'var'
getLocationsAndScales,ExpressionSet: no visible binding for global
  variable 'median'
getLocationsAndScales,ExpressionSet: no visible binding for global
  variable 'sd'
getLocationsAndScales,ExpressionSet: no visible binding for global
  variable 'mad'
likelihoodRatioSelection,ExpressionSet : <anonymous>: no visible global
  function definition for 'dnorm'
limmaSelection,ExpressionSet: no visible global function definition for
  'model.matrix'
medianDifferenceSelection,ExpressionSet: no visible binding for global
  variable 'median'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
  <anonymous>: no visible global function definition for 'dnorm'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous>: no
  visible binding for global variable 'classes'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  'largerClass'
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
  <anonymous> : <anonymous>: no visible binding for global variable
  'classes'
naiveBayesKernel,ExpressionSet: no visible binding for global variable
  'density'
naiveBayesKernel,ExpressionSet: no visible binding for global variable
  'featureValues'
naiveBayesKernel,ExpressionSet : <anonymous>: no visible global
  function definition for 'splinefun'
performancePlot,list: no visible global function definition for
  'reformulate'
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
  global variable 'expr'
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
  global variable '..density..'
previousSelection,ExpressionSet: no visible global function definition
  for 'na.omit'
rankingPlot,list: no visible global function definition for
  'reformulate'
runTests,ExpressionSet: no visible global function definition for
  'combn'
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'
selectionPlot,list: no visible global function definition for
  'reformulate'
subtractFromLocation,ExpressionSet: no visible binding for global
  variable 'median'
Undefined global functions or variables:
  ..density.. Class Freq Metric bartlett.test capture.output classes
  combn density dlda dnorm expr featureValues ks.test largerClass mad
  median model.matrix na.omit name predict reformulate sd splinefun
  type var
Consider adding
  importFrom("stats", "bartlett.test", "density", "dnorm", "ks.test",
             "mad", "median", "model.matrix", "na.omit", "predict",
             "reformulate", "sd", "splinefun", "var")
  importFrom("utils", "capture.output", "combn")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
runTest                    13.62   0.19   13.81
runTests                   11.52   0.34   17.14
edgeRselection             10.51   0.41   11.08
distribution                9.66   0.26   16.24
ClassifyResult-class        8.98   0.35   16.78
likelihoodRatioSelection    6.73   0.03    6.77
DMDselection                6.33   0.03    6.36
KolmogorovSmirnovSelection  6.33   0.01    6.34
KullbackLeiblerSelection    5.69   0.00    5.69
previousSelection           0.13   0.00    9.47
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
edgeRselection             10.41   0.12   10.53
ClassifyResult-class        9.74   0.33   18.70
distribution                8.89   0.41   15.58
runTest                     8.43   0.14    8.56
KolmogorovSmirnovSelection  8.38   0.00    8.37
DMDselection                6.96   0.04    7.00
likelihoodRatioSelection    6.94   0.03    6.97
runTests                    6.56   0.19   13.93
KullbackLeiblerSelection    5.65   0.00    5.66
previousSelection           0.13   0.02    9.50
* 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-3.6-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.

Installation output

ClassifyR.Rcheck/00install.out


install for i386

* installing *source* package 'ClassifyR' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'performance' in package 'ClassifyR'
** help
*** installing help indices
  converting help for package 'ClassifyR'
    finding HTML links ... done
    ClassifyResult-class                    html  
    DMDselection                            html  
    finding level-2 HTML links ... done

    KolmogorovSmirnovSelection              html  
    KullbackLeiblerSelection                html  
    PredictParams-class                     html  
    ROCplot                                 html  
    ResubstituteParams-class                html  
    SelectParams-class                      html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0wHupk/R.INSTALL221c55ee72e0/ClassifyR/man/SelectParams-class.Rd:30: missing file link 'ExpressionSet'
    SelectResult-class                      html  
    TrainParams-class                       html  
    TransformParams-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0wHupk/R.INSTALL221c55ee72e0/ClassifyR/man/TransformParams-class.Rd:22: missing file link 'ExpressionSet'
    bartlettSelection                       html  
    calcPerformance                         html  
    classifyInterface                       html  
    distribution                            html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0wHupk/R.INSTALL221c55ee72e0/ClassifyR/man/distribution.Rd:32: missing file link 'stat_density'
    edgeRselection                          html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp0wHupk/R.INSTALL221c55ee72e0/ClassifyR/man/edgeRselection.Rd:40: missing file link 'edgeR'
    fisherDiscriminant                      html  
    functionOrList-class                    html  
    getLocationsAndScales                   html  
    leveneSelection                         html  
    likelihoodRatioSelection                html  
    limmaSelection                          html  
    medianDifferenceSelection               html  
    mixmodels                               html  
    naiveBayesKernel                        html  
    nearestShrunkenCentroidPredictInterface
                                            html  
    nearestShrunkenCentroidSelectionInterface
                                            html  
    nearestShrunkenCentroidTrainInterface   html  
    pamrtrained-class                       html  
    performancePlot                         html  
    plotFeatureClasses                      html  
    previousSelection                       html  
    rankingPlot                             html  
    runTest                                 html  
    runTests                                html  
    samplesMetricMap                        html  
    selectionPlot                           html  
    subtractFromLocation                    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_1.12.2.zip
* DONE (ClassifyR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

ClassifyR.Rcheck/examples_i386/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 8.98 0.3516.78
DMDselection6.330.036.36
KolmogorovSmirnovSelection6.330.016.34
KullbackLeiblerSelection5.690.005.69
PredictParams-class000
ROCplot1.780.021.80
ResubstituteParams-class000
SelectParams-class000
SelectResult-class000
TrainParams-class000
TransformParams-class000
bartlettSelection0.600.010.61
calcPerformance0.010.000.02
classifyInterface0.670.070.75
distribution 9.66 0.2616.24
edgeRselection10.51 0.4111.08
fisherDiscriminant0.020.030.04
functionOrList-class000
getLocationsAndScales0.030.000.03
leveneSelection1.340.031.37
likelihoodRatioSelection6.730.036.77
limmaSelection0.900.000.91
medianDifferenceSelection0.530.000.53
mixmodels3.720.014.33
naiveBayesKernel0.640.000.64
nearestShrunkenCentroidPredictInterface0.240.030.26
nearestShrunkenCentroidSelectionInterface0.400.000.41
nearestShrunkenCentroidTrainInterface0.110.000.11
pamrtrained-class0.070.000.06
performancePlot1.790.001.80
plotFeatureClasses2.50.02.5
previousSelection0.130.009.47
rankingPlot1.970.024.17
runTest13.62 0.1913.81
runTests11.52 0.3417.14
samplesMetricMap1.040.021.06
selectionPlot2.210.004.38
subtractFromLocation0.080.000.07

ClassifyR.Rcheck/examples_x64/ClassifyR-Ex.timings

nameusersystemelapsed
ClassifyResult-class 9.74 0.3318.70
DMDselection6.960.047.00
KolmogorovSmirnovSelection8.380.008.37
KullbackLeiblerSelection5.650.005.66
PredictParams-class000
ROCplot2.170.022.19
ResubstituteParams-class000
SelectParams-class0.020.000.02
SelectResult-class000
TrainParams-class0.010.000.01
TransformParams-class000
bartlettSelection0.770.000.77
calcPerformance0.030.000.03
classifyInterface1.050.091.14
distribution 8.89 0.4115.58
edgeRselection10.41 0.1210.53
fisherDiscriminant0.040.000.03
functionOrList-class0.010.000.02
getLocationsAndScales0.030.000.03
leveneSelection1.310.041.34
likelihoodRatioSelection6.940.036.97
limmaSelection0.670.000.67
medianDifferenceSelection0.490.000.49
mixmodels3.150.003.89
naiveBayesKernel0.50.00.5
nearestShrunkenCentroidPredictInterface0.180.030.20
nearestShrunkenCentroidSelectionInterface0.280.000.28
nearestShrunkenCentroidTrainInterface0.080.010.10
pamrtrained-class0.040.000.04
performancePlot1.240.001.24
plotFeatureClasses2.830.002.82
previousSelection0.130.029.50
rankingPlot1.430.003.67
runTest8.430.148.56
runTests 6.56 0.1913.93
samplesMetricMap0.780.000.78
selectionPlot1.720.003.86
subtractFromLocation0.060.000.06