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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL miRspongeR
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘miRspongeR’ ...
** this is package ‘miRspongeR’ version ‘2.13.4’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c OCG_algorithm.c -o OCG_algorithm.o
OCG_algorithm.c: In function ‘getOCGclusters’:
OCG_algorithm.c:568:2: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  568 |  for(j=0;j<CardMax;j++)
      |  ^~~
OCG_algorithm.c:571:3: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  571 |   k=0;
      |   ^
OCG_algorithm.c:445:52: warning: variable ‘flag3’ set but not used [-Wunused-but-set-variable]
  445 |   int   NbY, Nl, Long, NewLong, cli, flag1, flag2, flag3;
      |                                                    ^~~~~
OCG_algorithm.c:790:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  790 |     for (j=0; j<i; j++)
      |     ^~~
OCG_algorithm.c:794:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  794 |       for (k=0; k<N; k++) Clas[k]=0;
      |       ^~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c complex.c -o complex.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c edge_duplicates.cpp -o edge_duplicates.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_edgesims.cpp -o linkcomm_edgesims.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_edgesims_all.cpp -o linkcomm_edgesims_all.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_functions.cpp -o linkcomm_functions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_hclust.cpp -o linkcomm_hclust.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c linkcomm_init.c -o linkcomm_init.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcomm_linkdensities.cpp -o linkcomm_linkdensities.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c linkcommhclust_order.cpp -o linkcommhclust_order.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c read_OCG.cpp -o read_OCG.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.22-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o miRspongeR.so OCG_algorithm.o complex.o edge_duplicates.o linkcomm_edgesims.o linkcomm_edgesims_all.o linkcomm_functions.o linkcomm_hclust.o linkcomm_init.o linkcomm_linkdensities.o linkcommhclust_order.o read_OCG.o registerDynamicSymbol.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-miRspongeR/00new/miRspongeR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘biomaRt::select’ by ‘dplyr::select’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::combine’ by ‘dplyr::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘cvms::font’ by ‘ggpubr::font’ when loading ‘SPONGE’
Warning: replacing previous import ‘ggplot2::margin’ by ‘randomForest::margin’ when loading ‘SPONGE’
Warning: replacing previous import ‘dplyr::combine’ by ‘randomForest::combine’ when loading ‘SPONGE’
Warning: replacing previous import ‘Biobase::exprs’ by ‘rlang::exprs’ when loading ‘SPONGE’
Warning: replacing previous import ‘rlang::exprs’ by ‘Biobase::exprs’ when loading ‘SPONGE’
** testing if installed package keeps a record of temporary installation path
* DONE (miRspongeR)