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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL mitoClone2
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'mitoClone2' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
../inst/SCITEpkg/findBestTrees.cpp:56:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch]
 double gamma = 1;
        ^~~~~
../inst/SCITEpkg/mcmcBinTreeMove.cpp: In function 'int pickNodeToMove(int*, int)':
../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
mkdir -p "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment]
  /**************************************************************************************
   
bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment]
 /**********************************************************************
  
bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable]
      int bc_absent;
          ^~~~~~~~~
bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable]
     hts_itr_t *iter = NULL;
                ^~~~
bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable]
     int c = 0;
         ^
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -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-mitoClone2/00new/mitoClone2/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mitoClone2'
    finding HTML links ... done
    bam2R_10x                               html  
    baseCountsFromBamList                   html  
    clusterMetaclones                       html  
    data                                    html  
    getAlleleCount                          html  
    getCloneLikelihood                      html  
    getVarsCandidate                        html  
    mitoPlot                                html  
    mut2GR                                  html  
    mutationCalls-class                     html  
    mutationCallsFromCohort                 html  
    mutationCallsFromExclusionlist          html  
    mutationCallsFromMatrix                 html  
    overwriteMetaclones                     html  
    plotClones                              html  
    pullcountsVars                          html  
    quick_cluster                           html  
    removeWindow                            html  
    setVarsCandidate                        html  
    varCluster                              html  
*** copying figures
** 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 (mitoClone2)
Making 'packages.html' ... done