##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL fgsea
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘fgsea’ ...
** this is package ‘fgsea’ version ‘1.37.4’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ScoreRuler.cpp -o ScoreRuler.o
ScoreRuler.cpp: In member function ‘void ScoreRuler::extend(double, int, double)’:
ScoreRuler.cpp:76:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   76 |         for (moves = 0; moves < sampleSize * genesetSize;) {
      |                         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const Rcpp::NumericVector&, const Rcpp::List&, const Rcpp::IntegerVector&)’:
fastGSEA.cpp:449:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  449 |         for (int j = 0; j < S.size(); ++j) {
      |                         ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fgseaMultilevel.cpp -o fgseaMultilevel.o
fgseaMultilevel.cpp: In function ‘Rcpp::DataFrame fgseaMultilevelCpp(const Rcpp::NumericVector&, SEXPREC* const&, int, int, int, double, bool, double, bool)’:
fgseaMultilevel.cpp:15:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   15 |     for (int i = 0; i < posRanks.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp: In member function ‘bool EsRuler::resampleGenesets(random_engine_t&)’:
fgseaMultilevelSupplement.cpp:64:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   64 |     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
      |                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:76:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   76 |     for (int sampleId = 0; sampleId < sampleSize; sampleId++){
      |                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:84:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   84 |         while (startFrom < sampleSize && get<0>(stats[startFrom]) == get<0>(stats[0])) {
      |                ~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   89 |     if (startFrom == sampleSize) {
      |         ~~~~~~~~~~^~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:101:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  101 |     for (int i = startFrom; i < sampleSize; ++i) {
      |                             ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  116 |     for (int i = startFrom; i < sampleSize; ++i) {
      |                             ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::extend(double, int, double)’:
fgseaMultilevelSupplement.cpp:144:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  144 |     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
      |                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:180:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  180 |             for (int j = 0; j < sampleSize; ++j) {
      |                             ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:187:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  187 |         for (int i = 0; i < sampleSize; ++i) {
      |                         ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:206:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  206 |             for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
      |                                    ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:212:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  212 |             for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
      |                                    ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:217:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
  217 |         for (int i = 0; i < sampleSize; ++i) {
      |                         ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘std::tuple<double, bool, double> EsRuler::getPvalue(double, double, bool)’:
fgseaMultilevelSupplement.cpp:246:15: warning: unused variable ‘n’ [-Wunused-variable]
  246 |     int const n = (int) ranks.size();
      |               ^
fgseaMultilevelSupplement.cpp:247:15: warning: unused variable ‘k’ [-Wunused-variable]
  247 |     int const k = pathwaySize;
      |               ^
fgseaMultilevelSupplement.cpp: In member function ‘EsRuler::PerturbateResult EsRuler::perturbate_until(const std::vector<long int>&, int, SampleChunks&, gsea_t, random_engine_t&, const std::function<bool(int, int)>&)’:
fgseaMultilevelSupplement.cpp:435:14: warning: unused variable ‘fl’ [-Wunused-variable]
  435 |         bool fl = false;
      |              ^~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c geseca.cpp -o geseca.o
geseca.cpp: In function ‘Rcpp::List gesecaCpp(const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, unsigned int, unsigned int, int, double)’:
geseca.cpp:9:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
    9 |     for (unsigned i = 0; i < E.nrow(); i++){
      |                          ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.23-bioc-rapid/R/include" -DNDEBUG  -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c util.cpp -o util.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library/00LOCK-fgsea/00new/fgsea/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (fgsea)