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###
### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL IRISFGM
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'IRISFGM' ...
** 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"C:/extsoft/include"  -fopenmp -DVER=2.08   -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"  -fopenmp -DVER=2.08   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c cluster.cpp -o cluster.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"  -fopenmp -DVER=2.08   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c expand.cpp -o expand.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"  -fopenmp -DVER=2.08   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c get_options.cpp -o get_options.o
"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 getline.c -o getline.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"  -fopenmp -DVER=2.08   -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"  -fopenmp -DVER=2.08   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c make_graph.cpp -o make_graph.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"  -fopenmp -DVER=2.08   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rcpp_irisfgm.cpp -o rcpp_irisfgm.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"  -fopenmp -DVER=2.08   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c read_array.cpp -o read_array.o
read_array.cpp: In function 'void discretize_new(const char*)':
read_array.cpp:882:21: warning: format '%d' expects argument of type 'int', but argument 4 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
         fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
                     ^~~~~~~
read_array.cpp:883:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         for (std::size_t j = 0; j < cols; j++) {
                                 ~~^~~~~~
read_array.cpp: In function 'void discretize_rpkm(const char*)':
read_array.cpp:1376:21: warning: format '%d' expects argument of type 'int', but argument 4 has type '__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type' {aka 'long long unsigned int'} [-Wformat=]
         fprintf(F2, "%s_%d", genes_n[id], eflags[id][i]);
                     ^~~~~~~
read_array.cpp:1377:35: warning: comparison of integer expressions of different signedness: 'std::size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
         for (std::size_t j = 0; j < cols; j++) {
                                 ~~^~~~~~
"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"  -fopenmp -DVER=2.08   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c struct.cpp -o struct.o
struct.cpp: In function 'void uglyTime(const char*, ...)':
struct.cpp:75:15: warning: variable 'lastTime' set but not used [-Wunused-but-set-variable]
   static long lastTime = 0;
               ^~~~~~~~
"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"  -fopenmp -DVER=2.08   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c write_block.cpp -o write_block.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o IRISFGM.dll tmp.def RcppExports.o cluster.o expand.o get_options.o getline.o main.o make_graph.o rcpp_irisfgm.o read_array.o struct.o write_block.o -fopenmp -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-IRISFGM/00new/IRISFGM/libs/x64
** R
** data
** byte-compile and prepare package for lazy loading
Creating a generic function from function 'ReadFrom10X_h5' in package 'IRISFGM'
Creating a generic function from function 'ReadFrom10X_folder' in package 'IRISFGM'
** help
*** installing help indices
  converting help for package 'IRISFGM'
    finding HTML links ... done
    AddMeta                                 html  
    BIC_LTMG                                html  
    BIC_ZIMG                                html  
    CLUSTERING                              html  
    CalBinaryMultiSignal                    html  
    CalBinarySingleSignal                   html  
    CreateIRISFGMObject                     html  
    DimReduce-class                         html  
    DotPlotPathway                          html  
    FindClassBasedOnMC                      html  
    FindGlobalMarkers                       html  
    finding level-2 HTML links ... done

    FindMarker                              html  
    Fit_LTMG                                html  
    GRAPH                                   html  
    GetBinaryMultiSignal                    html  
    GetBinarySingleSignal                   html  
    GetLTMGmatrix                           html  
    Global_Zcut                             html  
    IRISFGM-class                           html  
    InverseMillsRatio                       html  
    KS_LTMG                                 html  
    KS_ZIMG                                 html  
    LTMG                                    html  
    LogSeparateKRpkmNew                     html  
    LogSeparateKRpkmNewLR                   html  
    MCL                                     html  
    MINUS                                   html  
    MIN_return                              html  
    Pi_Zj_Zcut_new                          html  
    PlotDimension                           html  
    PlotHeatmap                             html  
    PlotMarkerHeatmap                       html  
    PlotMeta                                html  
    PlotModuleNetwork                       html  
    PlotNetwork                             html  
    ProcessData                             html  
    Pure_CDF                                html  
    ReadFrom10X_folder                      html  
    ReadFrom10X_h5                          html  
    RunBicluster                            html  
    RunClassification                       html  
    RunDimensionReduction                   html  
    RunDiscretization                       html  
    RunLTMG                                 html  
    RunPathway                              html  
    SC                                      html  
    SeparateKRpkmNew                        html  
    SeparateKRpkmNew2                       html  
    SeparateKRpkmNewLR                      html  
    SeparateKRpkmNewLRPlus                  html  
    SeparateKRpkmNewp                       html  
    State_return                            html  
    SubsetData                              html  
    dot-IDConvert                           html  
    dot-RunGO                               html  
    dot-RunKEGG                             html  
    dot-generateNetObject                   html  
    dot-getBlock                            html  
    dot-runBiclusterBaseOnDiscretization    html  
    dot-runBiclusterBaseOnLTMG              html  
    dot-separateBic                         html  
    example_object                          html  
    getMeta                                 html  
    qubic                                   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 (IRISFGM)
Making 'packages.html' ... done