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### Running command:
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###   rm -rf MSA2dist.buildbin-libdir && mkdir MSA2dist.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=MSA2dist.buildbin-libdir MSA2dist_0.99.2.tar.gz
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* installing *source* package 'MSA2dist' ...
** 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/RcppThread/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.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/RcppThread/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rcpp_distSTRING.cpp -o rcpp_distSTRING.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/RcppThread/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rcpp_pairwiseDeletionAA.cpp -o rcpp_pairwiseDeletionAA.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/RcppThread/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rcpp_pairwiseDeletionDNA.cpp -o rcpp_pairwiseDeletionDNA.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o MSA2dist.dll tmp.def RcppExports.o rcpp_distSTRING.o rcpp_pairwiseDeletionAA.o rcpp_pairwiseDeletionDNA.o -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/meat/MSA2dist.buildbin-libdir/00LOCK-MSA2dist/00new/MSA2dist/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppThread::LdFlags' when loading 'MSA2dist'
** help
*** installing help indices
  converting help for package 'MSA2dist'
    finding HTML links ... done
    AAMatrix-data                           html  
    GENETIC_CODE_TCAG                       html  
    aabin2aastring                          html  
    aastring2aabin                          html  
    aastring2aln                            html  
    aastring2dist                           html  
    addmask2string                          html  
    addpop2string                           html  
    addpos2string                           html  
    addregion2string                        html  
    aln2aastring                            html  
    aln2dnastring                           html  
    cds2aa                                  html  
    codon2numberAMBIG                       html  
    codon2numberTCAG                        html  
    codonmat2pnps                           html  
    codonmat2xy                             html  
    compareCodons                           html  
    dnabin2dnastring                        html  
    dnastring2aln                           html  
    dnastring2codonmat                      html  
    dnastring2dist                          html  
    dnastring2dnabin                        html  
    dnastring2kaks                          html  
    getmask                                 html  
    getpos                                  html  
    globalDeletion                          html  
    granthamMatrix                          html  
    hiv-data                                html  
    iupac-data                              html  
    iupacMatrix                             html  
    popinteger                              html  
    popnames                                html  
    rcpp_distSTRING                         html  
    rcpp_pairwiseDeletionAA                 html  
    rcpp_pairwiseDeletionDNA                html  
    region                                  html  
    regionused                              html  
    string2region                           html  
    subString                               html  
    uptriidx                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppThread::LdFlags' when loading 'MSA2dist'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'Rcpp::LdFlags' by 'RcppThread::LdFlags' when loading 'MSA2dist'
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'MSA2dist' as MSA2dist_0.99.2.zip
* DONE (MSA2dist)