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###
### Running command:
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###   rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lumi.buildbin-libdir lumi_2.42.0.tar.gz
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install for i386

* installing *source* package 'lumi' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** help
*** installing help indices
  converting help for package 'lumi'
    finding HTML links ... done
    IlluminaID2nuID                         html  
    LumiBatch-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:44: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:46: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:83: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:84: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:85: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:86: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:103: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:104: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:104: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:106: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:113: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/LumiBatch-class.Rd:113: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
    MAplot-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/MAplot-methods.Rd:16: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    addAnnotationInfo                       html  
    addControlData2lumi                     html  
    addControlData2methyLumiM               html  
    addNuID2lumi                            html  
    adjColorBias.quantile                   html  
    adjColorBias.ssn                        html  
    asBigMatrix-methods                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/asBigMatrix-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    beta2m                                  html  
    bgAdjust                                html  
    bgAdjustMethylation                     html  
    boxplot-MethyLumiM-methods              html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/boxplot-MethyLumiM-methods.Rd:16: file link 'bwplot' in package 'lattice' does not exist and so has been treated as a topic
    boxplot-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/boxplot-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    boxplotColorBias                        html  
    colorBiasSummary                        html  
    density-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/density-methods.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    detectOutlier                           html  
    detectionCall                           html  
    estimateBeta                            html  
    estimateIntensity                       html  
    estimateLumiCV                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/estimateLumiCV.Rd:17: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    estimateM                               html  
    estimateMethylationBG                   html  
    example.lumi                            html  
    example.lumiMethy                       html  
    example.methyTitration                  html  
    gammaFitEM                              html  
    getChipInfo                             html  
    getChrInfo                              html  
    getControlData                          html  
    getControlProbe                         html  
    getControlType                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/getControlType.Rd:20: file link 'controlTypes' in package 'methylumi' does not exist and so has been treated as a topic
    getNuIDMappingInfo                      html  
    hist-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/hist-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    id2seq                                  html  
    importMethyIDAT                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/importMethyIDAT.Rd:7: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/importMethyIDAT.Rd:20: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/importMethyIDAT.Rd:23: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/importMethyIDAT.Rd:37: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
    inverseVST                              html  
    is.nuID                                 html  
    lumi.package                            html  
    lumiB                                   html  
    lumiExpresso                            html  
    lumiMethyB                              html  
    lumiMethyC                              html  
    lumiMethyN                              html  
    lumiMethyR                              html  
    lumiMethyStatus                         html  
    lumiN                                   html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/lumiN.Rd:19: missing file link 'vsn'
    lumiQ                                   html  
    lumiR                                   html  
    lumiR.batch                             html  
    lumiT                                   html  
    m2beta                                  html  
    methylationCall                         html  
    monoSmu                                 html  
    monoSpline                              html  
    normalizeMethylation.quantile           html  
    normalizeMethylation.ssn                html  
    nuID2EntrezID                           html  
    nuID2IlluminaID                         html  
    nuID2RefSeqID                           html  
    nuID2probeID                            html  
    nuID2targetID                           html  
    pairs-methods                           html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/pairs-methods.Rd:16: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    plot-methods                            html  
    plotCDF                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/plotCDF.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/plotCDF.Rd:29: file link 'plot.ecdf' in package 'stats' does not exist and so has been treated as a topic
    plotColorBias1D                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/plotColorBias1D.Rd:21: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    plotColorBias2D                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/plotColorBias2D.Rd:24: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    plotControlData                         html  
    plotDensity                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/plotDensity.Rd:14: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    plotGammaFit                            html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/plotGammaFit.Rd:22: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    plotHousekeepingGene                    html  
    plotSampleRelation                      html  
    plotStringencyGene                      html  
    plotVST                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOkRsEH/R.INSTALL6b0261c75be/lumi/man/plotVST.Rd:17: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    probeID2nuID                            html  
    produceGEOPlatformFile                  html  
    produceGEOSampleInfoTemplate            html  
    produceGEOSubmissionFile                html  
    produceMethylationGEOSubmissionFile     html  
    rankinvariant                           html  
    rsn                                     html  
    seq2id                                  html  
    smoothQuantileNormalization             html  
    ssn                                     html  
    targetID2nuID                           html  
    vst                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package can be loaded from final location
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'lumi' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'lumi' as lumi_2.42.0.zip
* DONE (lumi)