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###
### Running command:
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###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch esATAC
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* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
* installing *source* package 'esATAC' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BedLine.cpp -o BedLine.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BedUtils.cpp -o BedUtils.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ChrDivi.cpp -o ChrDivi.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CutCountPre.cpp -o CutCountPre.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c CutSiteCount.cpp -o CutSiteCount.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c LibComplexQC.cpp -o LibComplexQC.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SortBed.cpp -o SortBed.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rcpp_wrapper.cpp -o rcpp_wrapper.o
rcpp_wrapper.cpp: In function 'int CutSiteCount_wrapper(Rcpp::List)':
rcpp_wrapper.cpp:334:7: warning: variable 'tmp_k' set but not used [-Wunused-but-set-variable]
   int tmp_k;
       ^~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c renamer.cpp -o renamer.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -DNDEBUG -DPLF_SYS_WIN -DR_EVN_FLAG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sam2bed.cc -o sam2bed.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o esATAC.dll tmp.def BedLine.o BedUtils.o ChrDivi.o CutCountPre.o CutSiteCount.o LibComplexQC.o RcppExports.o SortBed.o rcpp_wrapper.o renamer.o sam2bed.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.13-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'esATAC'
    finding HTML links ... done
    ATACProc-class                          html  
    BamToBed                                html  
    BedToBigWig                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bedToBigWig.html
    BedUtils                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bedUtils.html
    Bowtie2Mapping                          html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/bowtie2Mapping.html
    finding level-2 HTML links ... done

    CutSiteCountR                           html  
    CutSitePre                              html  
    FRiPQC                                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/fripQC.html
    FastQC                                  html  
    FindAdapter                             html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/findAdapter.html
    FragLenDistr                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/fragLenDistr.html
    LibComplexQC                            html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/libComplexQC.html
    PeakCallingFseq                         html  
    PeakQC                                  html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/peakQC.html
    RGo                                     html  
    RMotifScan                              html  
    RMotifScanPair                          html  
    RPeakAnno                               html  
    RPeakComp                               html  
    RSNPs                                   html  
    RemoveAdapter                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/removeAdapter.html
    Renamer                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/renamer.html
    Rsortbam                                html  
    SamToBam                                html  
    SamToBed                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/samToBed.html
    SingleRepReport                         html  
    TSSQC                                   html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/tssQC.html
    UnzipAndMerge                           html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/R/library/00LOCK-esATAC/00new/esATAC/help/unzipAndMerge.html
    atacPipe2                               html  
    atacRepsPipe                            html  
    atacRepsPipe2                           html  
    esATAC-package                          html  
    getMotifInfo                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package can be loaded from final location
Warning in options(stringsAsFactors = TRUE) :
  'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
** testing if installed package keeps a record of temporary installation path
* DONE (esATAC)
Making 'packages.html' ... done