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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL GBScleanR
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'GBScleanR' ...
** 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/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c GBSR_HMM.cpp -o GBSR_HMM.o
GBSR_HMM.cpp: In function 'std::vector<double> calcGenoprob(const double&, const double&, const double&, const double&, const double&, const double&, const int&)':
GBSR_HMM.cpp:206:16: warning: 'sum_prob' may be used uninitialized in this function [-Wmaybe-uninitialized]
       sum_prob += prob[g];
"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/RcppParallel/include'   -I"C:/extsoft/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o GBScleanR.dll tmp.def GBSR_HMM.o RcppExports.o -LD:/biocbuild/bbs-3.15-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -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-GBScleanR/00new/GBScleanR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GBScleanR'
    finding HTML links ... done
    GBScleanR                               html  
    GbsrGenotypeData-class                  html  
    finding level-2 HTML links ... done

    GbsrScheme-class                        html  
    addScan                                 html  
    addScheme                               html  
    boxplotGBSR                             html  
    calcReadStats                           html  
    closeGDS                                html  
    countGenotype                           html  
    countRead                               html  
    estGeno                                 html  
    gbsrGDS2CSV                             html  
    gbsrGDS2VCF                             html  
    gbsrVCF2GDS                             html  
    getAlleleA                              html  
    getAlleleB                              html  
    getChromosome                           html  
    getCountAlleleAlt                       html  
    getCountAlleleMissing                   html  
    getCountAlleleRef                       html  
    getCountGenoAlt                         html  
    getCountGenoHet                         html  
    getCountGenoMissing                     html  
    getCountGenoRef                         html  
    getCountRead                            html  
    getCountReadAlt                         html  
    getCountReadRef                         html  
    getFlipped                              html  
    getGenotype                             html  
    getHaplotype                            html  
    getInfo                                 html  
    getMAC                                  html  
    getMAF                                  html  
    getMeanReadAlt                          html  
    getMeanReadRef                          html  
    getParents                              html  
    getPloidy                               html  
    getPosition                             html  
    getQtileReadAlt                         html  
    getQtileReadRef                         html  
    getRead                                 html  
    getSDReadAlt                            html  
    getSDReadRef                            html  
    getScanID                               html  
    getSnpID                                html  
    getValidScan                            html  
    getValidSnp                             html  
    hasFlipped                              html  
    histGBSR                                html  
    initScheme                              html  
    isOpenGDS                               html  
    loadGDS                                 html  
    loadScanAnnot                           html  
    loadSnpAnnot                            html  
    nscan                                   html  
    nsnp                                    html  
    openGDS                                 html  
    pairsGBSR                               html  
    plotDosage                              html  
    plotGBSR                                html  
    plotReadRatio                           html  
    resetFilters                            html  
    resetScanFilters                        html  
    resetSnpFilters                         html  
    saveScanAnnot                           html  
    saveSnpAnnot                            html  
    setCallFilter                           html  
    setFiltGenotype                         html  
    setInfoFilter                           html  
    setParents                              html  
    setRawGenotype                          html  
    setScanFilter                           html  
    setSnpFilter                            html  
    setValidScan                            html  
    setValidSnp                             html  
    showScheme                              html  
    subsetGDS                               html  
    thinMarker                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GBScleanR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'staRank' is missing or broken
 done