##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BioQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘BioQC’ ...
** this is package ‘BioQC’ version ‘1.39.0’
** 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-3.23-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.23-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c gini.c -o gini.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.23-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.23-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c read_gmt.cpp -o read_gmt.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.23-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c stat_rank.c -o stat_rank.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG `/home/biocbuild/bbs-3.23-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c wmw_test.c -o wmw_test.o
'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
wmw_test.c: In function ‘wmw_test_list’:
wmw_test.c:118: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  118 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘wmw_test’:
wmw_test.c:168: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  168 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘signed_wmw_test_list’:
wmw_test.c:201: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  201 | #pragma omp parallel for
      | 
wmw_test.c: In function ‘signed_wmw_test’:
wmw_test.c:270: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
  270 | #pragma omp parallel for
      | 
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-BioQC/00new/BioQC/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BioQC)