##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CellaRepertorium
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CellaRepertorium' ...
** 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"     -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 cdhit-bombs.cpp -o cdhit-bombs.o
In file included from cdhit-bombs.cpp:2:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ~~~~~^~~~~~~~~~~~~~~~~~~~
"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 cdhit-common.cpp -o cdhit-common.o
cdhit-common.cpp:160: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
   #pragma omp critical
 
cdhit-common.cpp:174: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
  #pragma omp critical
 
cdhit-common.cpp:2418: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:2435: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:2437: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
     #pragma omp flush (stop)
 
cdhit-common.cpp:2458: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
        #pragma omp critical
 
cdhit-common.cpp:2467: warning: ignoring #pragma omp flush [-Wunknown-pragmas]
        #pragma omp flush (stop)
 
cdhit-common.cpp:2492: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
     #pragma omp parallel for schedule( dynamic, 1 )
 
cdhit-common.cpp:3151: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for schedule( dynamic, 1 )
 
In file included from cdhit-common.cpp:37:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ~~~~~^~~~~~~~~~~~~~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:545:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
  int max_diag = 0;
      ^~~~~~~~
cdhit-common.cpp: In function 'int diag_test_aapn_est(int, char*, int, int, WorkingBuffer&, int&, int, int&, int&, int&, int)':
cdhit-common.cpp:669:6: warning: variable 'max_diag' set but not used [-Wunused-but-set-variable]
  int max_diag = 0;
      ^~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::SortDivide(Options&, bool)':
cdhit-common.cpp:1774:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if (len > max_len) max_len = len;
       ~~~~^~~~~~~~~
cdhit-common.cpp:1775:11: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   if (len < min_len) min_len = len;
       ~~~~^~~~~~~~~
cdhit-common.cpp: In member function 'void SequenceDB::DoClustering(int, const Options&)':
cdhit-common.cpp:2379:9: warning: variable 'mem' set but not used [-Wunused-but-set-variable]
  size_t mem, mega = 1000000;
         ^~~
"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 cdhit-est.cpp -o cdhit-est.o
In file included from cdhit-est.cpp:32:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ~~~~~^~~~~~~~~~~~~~~~~~~~
"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 cdhit.cpp -o cdhit.o
In file included from cdhit.cpp:31:
cdhit-common.h: In member function 'void WorkingBuffer::Set(size_t, size_t, const Options&)':
cdhit-common.h:494:12: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'const int' [-Wsign-compare]
   if( band > options.band_width ) band = options.band_width;
       ~~~~~^~~~~~~~~~~~~~~~~~~~
"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 progress.cpp -o progress.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CellaRepertorium.dll tmp.def RcppExports.o cdhit-bombs.o cdhit-common.o cdhit-est.o cdhit.o progress.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-CellaRepertorium/00new/CellaRepertorium/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CellaRepertorium'
    finding HTML links ... done
    ContigCellDB-fun                        html  
    canonicalize_cell                       html  
    canonicalize_cluster                    html  
    cash-ContigCellDB-method                html  
    ccdb_ex                                 html  
    ccdb_join                               html  
    cdhit                                   html  
    cdhit_ccdb                              html  
    cland                                   html  
    cluster_filterset                       html  
    cluster_germline                        html  
    cluster_logistic_test                   html  
    cluster_permute_test                    html  
    cluster_plot                            html  
    contigs_qc                              html  
    cross_tab_tbl                           html  
    crosstab_by_celltype                    html  
    dot-cluster_permute_test                html  
    entropy                                 html  
    enumerate_pairing                       html  
    equalize_ccdb                           html  
    fancy_name_contigs                      html  
    fine_cluster_seqs                       html  
    fine_clustering                         html  
    generate_pseudobulk                     html  
    guess_celltype                          html  
    hushWarning                             html  
    left_join_warn                          html  
    map_axis_labels                         html  
    mutate_cdb                              html  
    pairing_tables                          html  
    plot_cluster_factors                    html  
    purity                                  html  
    rank_prevalence_ccdb                    html  
    rbind-ContigCellDB-method               html  
    split_cdb                               html  
    sub-sub-ContigCellDB-character-missing-method
                                            html  
*** copying figures
** 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 (CellaRepertorium)
Making 'packages.html' ... done