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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:IRISFGM.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings IRISFGM_1.3.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/IRISFGM.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IRISFGM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IRISFGM' version '1.3.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'IRISFGM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/IRISFGM/libs/x64/IRISFGM.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/IRISFGM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   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