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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL R3CPET
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'R3CPET' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R3CPET_init.c -o R3CPET_init.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"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"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c corpus.cpp -o corpus.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"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c main.cpp -o main.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"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c state.cpp -o state.o
state.cpp: In member function 'int HDP::sample_word_assignment(DocState*, int, bool, vct*)':
state.cpp:253:10: warning: 'k' may be used uninitialized in this function [-Wmaybe-uninitialized]
   return int(old_k != k);
          ^~~~~~~~~~~~~~~
"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"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c stirln.cpp -o stirln.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"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c utils.cpp -o utils.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o R3CPET.dll tmp.def R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.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/R/library/00LOCK-R3CPET/00new/R3CPET/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
NOTE: arguments in definition for validity method for class 'ChromMaintainers' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'HLDAResult' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'NetworkCollection' changed from (x) to (object)
** help
*** installing help indices
  converting help for package 'R3CPET'
    finding HTML links ... done
    Biogrid                                 html  
    finding level-2 HTML links ... done

    ChiapetExperimentData-class             html  
    ChromMaintainers-class                  html  
    CreateCenteredBED-methods               html  
    EnsemblToHGNC                           html  
    EntrezToHGNC                            html  
    GOEnrich-methods                        html  
    GenerateNetworks-methods                html  
    HLDAResult-class                        html  
    HPRD                                    html  
    InferNetworks-methods                   html  
    NetworkCollection-class                 html  
    PrepareData-methods                     html  
    R3CPET-package                          html  
    RPKMS                                   html  
    annotateExpression-methods              html  
    buildNetworks-methods                   html  
    chromosoms                              html  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-R3CPET/00new/R3CPET/help/Chromosoms.html
    cluesOrSota-class                       html  
    clusterInteractions-methods             html  
    createIndexes-methods                   html  
    createServer-methods                    html  
    geneLocations                           html  
    getRegionsInNetwork-methods             html  
    getRegionsIncluster-methods             html  
    loadPETs-methods                        html  
    loadPPI-methods                         html  
    loadTFBS-methods                        html  
    outputGenesPerClusterToDir-methods      html  
    outputGenesPerNetworkToDir-methods      html  
    plotRes-methods                         html  
    plotTrack                               html  
    updateResults-methods                   html  
    visualizeCircos-methods                 html  
    visualizeInteractions-methods           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 (R3CPET)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'ELMER' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'maser' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'STAN' is missing or broken
 done