* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘ontologySimilarity’ ...
** this is package ‘ontologySimilarity’ version ‘2.7’
** package ‘ontologySimilarity’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmppJNXiO/R.INSTALL3eeb8c4525f287/ontologySimilarity/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Interface.cpp -o Interface.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c PVal.cpp -o PVal.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Sampling.cpp -o Sampling.o
Sampling.cpp: In function ‘bool next_combination(Rcpp::IntegerVector, size_t, int)’:
Sampling.cpp:16:23: warning: comparison of integer expressions of different signedness: ‘Rcpp::traits::storage_type<13>::type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   16 |         if (item[n-i] < N-i) {
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c SimMatrix.cpp -o SimMatrix.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c TermList.cpp -o TermList.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c TermSetSimData.cpp -o TermSetSimData.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o ontologySimilarity.so Interface.o PVal.o RcppExports.o Sampling.o SimMatrix.o TermList.o TermSetSimData.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmppJNXiO/R.INSTALL3eeb8c4525f287/ontologySimilarity/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmppJNXiO/R.INSTALL3eeb8c4525f287/ontologySimilarity/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmppJNXiO/R.INSTALL3eeb8c4525f287/ontologySimilarity/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-ontologySimilarity/00new/ontologySimilarity/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘ontologySimilarity’
    finding HTML links ... done
    GO_IC                                   html  
    create_sim_index                        html  
    descendants_IC                          html  
    gene_GO_terms                           html  
    get_asym_sim_grid                       html  
    get_profile_sims                        html  
    get_sim                                 html  
    get_sim_grid                            html  
    get_sim_p                               html  
    get_sim_p_from_ontology                 html  
    get_similarity_rank_matrix              html  
    get_term_set_to_term_sims               html  
    get_term_sim_mat                        html  
    group_term_enrichment                   html  
    lin                                     html  
    ontologySimilarity-package              html  
    resnik                                  html  
    sample_group_sim                        html  
    sample_group_sim_from_ontology          html  
** 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 (ontologySimilarity)