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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SNPRelate
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'SNPRelate' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ConvToGDS.cpp -o ConvToGDS.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_SNPRelate.c -o R_SNPRelate.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c SNPRelate.cpp -o SNPRelate.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ThreadPool.cpp -o ThreadPool.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dGenGWAS.cpp -o dGenGWAS.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c dVect.cpp -o dVect.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genBeta.cpp -o genBeta.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genEIGMIX.cpp -o genEIGMIX.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genFst.cpp -o genFst.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genHWE.cpp -o genHWE.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genIBD.cpp -o genIBD.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genIBS.cpp -o genIBS.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genKING.cpp -o genKING.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genLD.cpp -o genLD.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genPCA.cpp -o genPCA.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DUSING_R -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/gdsfmt/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c genSlideWin.cpp -o genSlideWin.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SNPRelate.dll tmp.def ConvToGDS.o R_SNPRelate.o SNPRelate.o ThreadPool.o dGenGWAS.o dVect.o genBeta.o genEIGMIX.o genFst.o genHWE.o genIBD.o genIBS.o genKING.o genLD.o genPCA.o genSlideWin.o -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -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-SNPRelate/00new/SNPRelate/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SNPRelate'
    finding HTML links ... done
    SNPGDSFileClass-class                   html  
    SNPRelate-package                       html  
    hapmap_geno                             html  
    snpgdsAdmixPlot                         html  
    snpgdsAdmixProp                         html  
    snpgdsAlleleSwitch                      html  
    snpgdsApartSelection                    html  
    snpgdsBED2GDS                           html  
    finding level-2 HTML links ... done

    snpgdsClose                             html  
    snpgdsCombineGeno                       html  
    snpgdsCreateGeno                        html  
    snpgdsCreateGenoSet                     html  
    snpgdsCutTree                           html  
    snpgdsDiss                              html  
    snpgdsDrawTree                          html  
    snpgdsEIGMIX                            html  
    snpgdsErrMsg                            html  
    snpgdsExampleFileName                   html  
    snpgdsFst                               html  
    snpgdsGDS2BED                           html  
    snpgdsGDS2Eigen                         html  
    snpgdsGDS2PED                           html  
    snpgdsGEN2GDS                           html  
    snpgdsGRM                               html  
    snpgdsGetGeno                           html  
    snpgdsHCluster                          html  
    snpgdsHWE                               html  
    snpgdsIBDKING                           html  
    snpgdsIBDMLE                            html  
    snpgdsIBDMLELogLik                      html  
    snpgdsIBDMoM                            html  
    snpgdsIBDSelection                      html  
    snpgdsIBS                               html  
    snpgdsIBSNum                            html  
    snpgdsIndInb                            html  
    snpgdsIndInbCoef                        html  
    snpgdsIndivBeta                         html  
    snpgdsLDMat                             html  
    snpgdsLDpair                            html  
    snpgdsLDpruning                         html  
    snpgdsMergeGRM                          html  
    snpgdsOpen                              html  
    snpgdsOption                            html  
    snpgdsPCA                               html  
    snpgdsPCACorr                           html  
    snpgdsPCASNPLoading                     html  
    snpgdsPCASampLoading                    html  
    snpgdsPED2GDS                           html  
    snpgdsPairIBD                           html  
    snpgdsPairIBDMLELogLik                  html  
    snpgdsPairScore                         html  
    snpgdsSNPList                           html  
    snpgdsSNPListClass                      html  
    snpgdsSNPListIntersect                  html  
    snpgdsSNPRateFreq                       html  
    snpgdsSampMissRate                      html  
    snpgdsSelectSNP                         html  
    snpgdsSlidingWindow                     html  
    snpgdsSummary                           html  
    snpgdsTranspose                         html  
    snpgdsVCF2GDS                           html  
    snpgdsVCF2GDS_R                         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 (SNPRelate)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'profileScoreDist' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'S4Vectors' is missing or broken
 done