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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL contiBAIT
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'contiBAIT' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c buildLinkageGroups.cpp -o buildLinkageGroups.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c computeSim.cpp -o computeSim.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-contiBAIT/00new/contiBAIT/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** help
*** installing help indices
  converting help for package 'contiBAIT'
    finding HTML links ... done
    BAIT                                    html  
    ChrTable                                html  
    ContigOrdering                          html  
    LibraryGroupList                        html  
    LinkageGroupList                        html  
    StrandFreqMatrix                        html  
    StrandReadMatrix                        html  
    StrandStateList                         html  
    StrandStateMatrix                       html  
    barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
                                            html  
    clusterContigs-StrandStateMatrix-method
                                            html  
    contiBAIT                               html  
    exampleChrTable                         html  
    exampleContigOrder                      html  
    exampleCrickFreq                        html  
    exampleDividedChr                       html  
    exampleLGList                           html  
    exampleLibList                          html  
    exampleReadCounts                       html  
    exampleStrandFreq                       html  
    exampleWCMatrix                         html  
    exampleWatsonFreq                       html  
    findSexGroups-LinkageGroupList-StrandStateMatrix-method
                                            html  
    findSimilarLibraries                    html  
    fixLinkageGroups                        html  
    flipOrderedLinkageGroups                html  
    highlightAssemblyErrors                 html  
    ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
                                            html  
    locateMisorients                        html  
    makeBoxPlot                             html  
    makeChrTable                            html  
    mapGapFromOverlap                       html  
    mergeFlankedLGs                         html  
    orderAllLinkageGroups                   html  
    orderContigsGreedy                      html  
    orderContigsTSP                         html  
    plotContigOrder                         html  
    plotLGDistances-LinkageGroupList-StrandStateMatrix-method
                                            html  
    plotWCdistribution-StrandFreqMatrix-method
                                            html  
    preprocessStrandTable-StrandFreqMatrix-method
                                            html  
    reorientAndMergeLGs                     html  
    show-ContigOrdering-method              html  
    show-LibraryGroupList-method            html  
    show-LinkageGroupList-method            html  
    show-OrientationFrame-method            html  
    show-StrandFreqMatrix-method            html  
    show-StrandReadMatrix-method            html  
    show-StrandStateList-method             html  
    show-StrandStateMatrix-method           html  
    strandSeqFreqTable                      html  
    thoroughBed                             html  
    writeBed                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package keeps a record of temporary installation path
* DONE (contiBAIT)
Making 'packages.html' ... done