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INSTALL report for limma on tokay2

This page was generated on 2018-10-17 08:31:52 -0400 (Wed, 17 Oct 2018).

Package 786/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
limma 3.36.5
Gordon Smyth
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/limma
Branch: RELEASE_3_7
Last Commit: 3148d1c
Last Changed Date: 2018-09-20 05:59:08 -0400 (Thu, 20 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  OK  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: limma
Version: 3.36.5
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/limma_3.36.5.tar.gz && rm -rf limma.buildbin-libdir && mkdir limma.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=limma.buildbin-libdir limma_3.36.5.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL limma_3.36.5.zip && rm limma_3.36.5.tar.gz limma_3.36.5.zip
StartedAt: 2018-10-16 18:36:53 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 18:39:40 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 167.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/limma_3.36.5.tar.gz && rm -rf limma.buildbin-libdir && mkdir limma.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=limma.buildbin-libdir limma_3.36.5.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL limma_3.36.5.zip && rm limma_3.36.5.tar.gz limma_3.36.5.zip
###
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install for i386

* installing *source* package 'limma' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c normexp.c -o normexp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c weighted_lowess.c -o weighted_lowess.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o limma.dll tmp.def init.o normexp.o weighted_lowess.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/limma.buildbin-libdir/limma/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'limma'
    finding HTML links ... done
    01Introduction                          html  
    02classes                               html  
    03reading                               html  
    04Background                            html  
    05Normalization                         html  
    06linearmodels                          html  
    07SingleChannel                         html  
    08Tests                                 html  
    09Diagnostics                           html  
    10GeneSetTests                          html  
    11RNAseq                                html  
    EList                                   html  
    LargeDataObject                         html  
    PrintLayout                             html  
    TestResults                             html  
    alias2Symbol                            html  
    anova-method                            html  
    arrayWeights                            html  
    arrayWeightsQuick                       html  
    asMatrixWeights                         html  
    asdataframe                             html  
    asmalist                                html  
    asmatrix                                html  
    auROC                                   html  
    avearrays                               html  
    avedups                                 html  
    avereps                                 html  
    backgroundcorrect                       html  
    barcodeplot                             html  
    beadCountWeights                        html  
    blockDiag                               html  
    bwss                                    html  
    bwss.matrix                             html  
    camera                                  html  
    cbind                                   html  
    changelog                               html  
    channel2M                               html  
    classifytests                           html  
    contrastAsCoef                          html  
    contrasts.fit                           html  
    controlStatus                           html  
    coolmap                                 html  
    cumOverlap                              html  
    decideTests                             html  
    detectionPValue                         html  
    diffSplice                              html  
    dim                                     html  
    dimnames                                html  
    dupcor                                  html  
    ebayes-deprecated                       html  
    ebayes                                  html  
    exprsMA                                 html  
    fitGammaIntercept                       html  
    fitfdist                                html  
    fitmixture                              html  
    fitted.MArrayLM                         html  
    genas                                   html  
    geneSetTest                             html  
    getEAWP                                 html  
    getSpacing                              html  
    getlayout                               html  
    gls.series                              html  
    goana                                   html  
    gridspotrc                              html  
    heatdiagram                             html  
    helpMethods                             html  
    ids2indices                             html  
    imageplot                               html  
    imageplot3by2                           html  
    intraspotCorrelation                    html  
    isfullrank                              html  
    isnumeric                               html  
    kooperberg                              html  
    limmaUsersGuide                         html  
    lm.series                               html  
    lmFit                                   html  
    lmscFit                                 html  
    loessfit                                html  
    logcosh                                 html  
    logsumexp                               html  
    ma3x3                                   html  
    makeContrasts                           html  
    makeunique                              html  
    malist                                  html  
    marraylm                                html  
    mdplot                                  html  
    merge                                   html  
    mergeScansRG                            html  
    modelMatrix                             html  
    modifyWeights                           html  
    mrlm                                    html  
    nec                                     html  
    normalizeCyclicLoess                    html  
    normalizeMedianAbsValues                html  
    normalizeRobustSpline                   html  
    normalizeVSN                            html  
    normalizeWithinArrays                   html  
    normalizebetweenarrays                  html  
    normalizeprintorder                     html  
    normalizequantiles                      html  
    normexpfit                              html  
    normexpfitcontrol                       html  
    normexpfitdetectionp                    html  
    normexpsignal                           html  
    plotDensities                           html  
    plotExons                               html  
    plotFB                                  html  
    plotMD                                  html  
    plotMDS                                 html  
    plotRLDF                                html  
    plotSA                                  html  
    plotSplice                              html  
    plotWithHighlights                      html  
    plotlines                               html  
    plotma                                  html  
    plotma3by2                              html  
    plotprinttiploess                       html  
    poolvar                                 html  
    predFCm                                 html  
    printHead                               html  
    printorder                              html  
    printtipWeights                         html  
    propTrueNull                            html  
    propexpr                                html  
    protectMetachar                         html  
    qqt                                     html  
    qualwt                                  html  
    rankSumTestwithCorrelation              html  
    read.columns                            html  
    read.idat                               html  
    read.ilmn                               html  
    read.ilmn.targets                       html  
    read.maimages                           html  
    readGPRHeader                           html  
    readImaGeneHeader                       html  
    readSpotTypes                           html  
    readTargets                             html  
    readgal                                 html  
    removeBatchEffect                       html  
    removeext                               html  
    residuals.MArrayLM                      html  
    rglist                                  html  
    roast                                   html  
    romer                                   html  
    selectmodel                             html  
    squeezeVar                              html  
    strsplit2                               html  
    subsetting                              html  
    summary                                 html  
    targetsA2C                              html  
    tmixture                                html  
    topGO                                   html  
    topRomer                                html  
    topSplice                               html  
    toptable                                html  
    tricubeMovingAverage                    html  
    trigammainverse                         html  
    trimWhiteSpace                          html  
    uniquegenelist                          html  
    unwrapdups                              html  
    venn                                    html  
    volcanoplot                             html  
    voom                                    html  
    voomWithQualityWeights                  html  
    vooma                                   html  
    weightedLowess                          html  
    weightedmedian                          html  
    writefit                                html  
    wsva                                    html  
    zscore                                  html  
** building package indices
** installing vignettes
   'intro.Rnw' 
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'limma' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c normexp.c -o normexp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c weighted_lowess.c -o weighted_lowess.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o limma.dll tmp.def init.o normexp.o weighted_lowess.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/limma.buildbin-libdir/limma/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'limma' as limma_3.36.5.zip
* DONE (limma)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'limma' successfully unpacked and MD5 sums checked
In R CMD INSTALL