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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL epigraHMM
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'epigraHMM' ...
** 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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c aggregate.cpp -o aggregate.o
aggregate.cpp: In function 'arma::mat aggregate(arma::vec, arma::vec)':
aggregate.cpp:26:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         while( index >= vec.size() ){
                ~~~~~~^~~~~~~~~~~~~
"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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c computeBIC.cpp -o computeBIC.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c computeQFunction.cpp -o computeQFunction.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c computeViterbiSequence.cpp -o computeViterbiSequence.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c consensusRejectionControlled.cpp -o consensusRejectionControlled.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c differentialRejectionControlled.cpp -o differentialRejectionControlled.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c expStep.cpp -o expStep.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c getMarginalProbability.cpp -o getMarginalProbability.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c innerMaxStepProb.cpp -o innerMaxStepProb.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c maxStepProb.cpp -o maxStepProb.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rbinomVectorized.cpp -o rbinomVectorized.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c reweight.cpp -o reweight.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/RcppArmadillo/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/include'   -I"C:/extsoft/include"  -fopenmp -DARMA_USE_HDF5   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c simulateMarkovChain.cpp -o simulateMarkovChain.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o epigraHMM.dll tmp.def RcppExports.o aggregate.o computeBIC.o computeQFunction.o computeViterbiSequence.o consensusRejectionControlled.o differentialRejectionControlled.o expStep.o getMarginalProbability.o innerMaxStepProb.o maxStepProb.o rbinomVectorized.o reweight.o simulateMarkovChain.o -LD:/biocbuild/bbs-3.15-bioc/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lszip -lz -lpsapi -fopenmp -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-epigraHMM/00new/epigraHMM/libs/x64
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'epigraHMM'
    finding HTML links ... done
    addOffsets                              html  
    callPatterns                            html  
    callPeaks                               html  
    cleanCounts                             html  
    controlEM                               html  
    epigraHMM                               html  
    epigraHMMDataSetFromBam                 html  
    epigraHMMDataSetFromMatrix              html  
    estimateTransitionProb                  html  
    expStep                                 html  
    helas3                                  html  
    info                                    html  
    initializer                             html  
    maxStepProb                             html  
    normalizeCounts                         html  
    plotCounts                              html  
    plotPatterns                            html  
    segmentGenome                           html  
    simulateMarkovChain                     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 (epigraHMM)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'consensusDE' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'transcriptR' is missing or broken
 done