* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘OjaNP’ ...
** this is package ‘OjaNP’ version ‘2.0’
** package ‘OjaNP’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-16 (Debian 16.2.0-1) 16.2.0’
using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOQHxuC/R.INSTALL35e7ae4c9f372f/OjaNP/src'
g++-16 -std=gnu++20 -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 Matrix2D.cpp -o Matrix2D.o
g++-16 -std=gnu++20 -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 SubsetGenerator.cpp -o SubsetGenerator.o
g++-16 -std=gnu++20 -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 _Vector.cpp -o _Vector.o
g++-16 -std=gnu++20 -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 algorithms.cpp -o algorithms.o
algorithms.cpp: In member function ‘OjaPoint OjaData::medianFollowIntersectionLines()’:
algorithms.cpp:280:13: warning: variable ‘fail_count’ set but not used [-Wunused-but-set-variable=]
  280 |         int fail_count = 0;
      |             ^~~~~~~~~~
algorithms.cpp: In member function ‘OjaPoint OjaData::medianBootstrap(const std::__cxx11::list<Hyperplane>&, const std::__cxx11::list<Index>&, const matrix&)’:
algorithms.cpp:1139:13: warning: variable ‘sets’ set but not used [-Wunused-but-set-variable=]
 1139 |         int sets=set_size; // Arvottavan setin koko
      |             ^~~~
g++-16 -std=gnu++20 -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 bounded_search.cpp -o bounded_search.o
bounded_search.cpp: In function ‘void addBound(Hyperplane&, bool, std::vector<Hyperplane>&, std::vector<Point>&, std::set<int>&, std::vector<std::set<int> >&, unsigned int)’:
bounded_search.cpp:104:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  104 |                 for (int k = 0; k < dim - 1; k++){
      |                                 ~~^~~~~~~~~
bounded_search.cpp:113:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Hyperplane>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  113 |                 for (int i = 0; i < bounds.size() - 1; i++){
      |                                 ~~^~~~~~~~~~~~~~~~~~~
bounded_search.cpp:127:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  127 |                 for (int k = 0; k < dim - 1; k++){
      |                                 ~~^~~~~~~~~
bounded_search.cpp:143:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Hyperplane>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  143 |         for (int i = 0; i < bounds.size(); i++){
      |                         ~~^~~~~~~~~~~~~~~
bounded_search.cpp: In function ‘void clearBounds(std::vector<Point>&, std::set<int>&, std::vector<std::set<int> >&)’:
bounded_search.cpp:171:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  171 |         for (i = 0; i < bounds_crossing_indexes.size(); i++){
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bounded_search.cpp:179:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Point>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  179 |         for (i = 0; i < crossing_points.size(); i++){ used_crossing_points.insert(i); }
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~
bounded_search.cpp: In member function ‘OjaPoint OjaData::medianFollowIntersectionLinesBounded()’:
bounded_search.cpp:476:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Point>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  476 |                 for (int j = 1; j < crossing_points.size(); j++){
      |                                 ~~^~~~~~~~~~~~~~~~~~~~~~~~
bounded_search.cpp:511:48: warning: suggest parentheses around ‘+’ in operand of ‘&’ [-Wparentheses]
  511 |                                 if (len != ((v + (v >> 4) & 0xF0F0F0F) * 0x1010101) >> 24) continue; // count set bits, check if the sequence is of desired length
      |                                              ~~^~~~~~~~~~
bounded_search.cpp:511:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘Int32’ {aka ‘unsigned int’} [-Wsign-compare]
  511 |                                 if (len != ((v + (v >> 4) & 0xF0F0F0F) * 0x1010101) >> 24) continue; // count set bits, check if the sequence is of desired length
      |                                     ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bounded_search.cpp:527:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Hyperplane>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  527 |                 for (int i = 0; i < bounds.size(); i++){
      |                                 ~~^~~~~~~~~~~~~~~
bounded_search.cpp:529:55: warning: comparison of integer expressions of different signedness: ‘std::set<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  529 |                         for (int a = 0; bci[i].size() < dim(); a++){
      |                                         ~~~~~~~~~~~~~~^~~~~~~
bounded_search.cpp:543:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Hyperplane>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  543 |                 for (int i = 0; i < bounds.size(); i++)
      |                                 ~~^~~~~~~~~~~~~~~
bounded_search.cpp:190:13: warning: variable ‘fail_count’ set but not used [-Wunused-but-set-variable=]
  190 |         int fail_count = 0;
      |             ^~~~~~~~~~
g++-16 -std=gnu++20 -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 data.cpp -o data.o
data.cpp: In member function ‘void Data::enlarge(const std::vector<Point>&)’:
data.cpp:161:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Point>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  161 |         for (int i = 0; i<Points.size(); i++)
      |                         ~^~~~~~~~~~~~~~
gcc-16 -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 -Wstrict-prototypes -pedantic -mtune=native  -c det.c -o det.o
g++-16 -std=gnu++20 -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 global.cpp -o global.o
g++-16 -std=gnu++20 -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 hyperplane.cpp -o hyperplane.o
hyperplane.cpp: In member function ‘void HyperplaneSet::get(const std::vector<Hyperplane>&)’:
hyperplane.cpp:370:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Hyperplane>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  370 |         for (int i = 0; i<hyperplanes.size(); i++)
      |                         ~^~~~~~~~~~~~~~~~~~~
g++-16 -std=gnu++20 -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 index.cpp -o index.o
index.cpp: In constructor ‘IndexSet::IndexSet(int, int, const std::vector<std::set<int> >&)’:
index.cpp:626:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::set<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  626 |         for (int i = 0; i < indexes.size(); i++)
      |                         ~~^~~~~~~~~~~~~~~~
g++-16 -std=gnu++20 -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++-16 -std=gnu++20 -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 lattice.cpp -o lattice.o
g++-16 -std=gnu++20 -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 line.cpp -o line.o
g++-16 -std=gnu++20 -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 matrix_wrapper.cpp -o matrix_wrapper.o
g++-16 -std=gnu++20 -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 misc.cpp -o misc.o
misc.cpp: In function ‘long unsigned int choices(int, int)’:
misc.cpp:65:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   65 |         while (d <= k){ r *= n--; r /= d++; }
      |                ~~^~~~
g++-16 -std=gnu++20 -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 oja_data.cpp -o oja_data.o
g++-16 -std=gnu++20 -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 oja_geometry.cpp -o oja_geometry.o
oja_geometry.cpp: In member function ‘std::set<int> DotSet::find_valid_bounds(std::set<int>&, const OjaData*, Point&)’:
oja_geometry.cpp:324:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<double, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  324 |                 for (i = 0; i < dotarray->size() - 1; i++){
      |                             ~~^~~~~~~~~~~~~~~~~~~~~~
oja_geometry.cpp:336:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<double, int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  336 |                 for (i = i + 1; i < dotarray->size() - 1; i++){
      |                                 ~~^~~~~~~~~~~~~~~~~~~~~~
oja_geometry.cpp: In member function ‘void OjaLine::get_random_through(int)’:
oja_geometry.cpp:764:9: warning: variable ‘last_try’ set but not used [-Wunused-but-set-variable=]
  764 |     int last_try = 1000;
      |         ^~~~~~~~
oja_geometry.cpp: In member function ‘void OjaLine::get_random_through(int, int)’:
oja_geometry.cpp:798:9: warning: variable ‘last_try’ set but not used [-Wunused-but-set-variable=]
  798 |     int last_try = 1000;
      |         ^~~~~~~~
oja_geometry.cpp: In member function ‘OjaPoint DotSet::min(double&)’:
oja_geometry.cpp:663:62: warning: ‘min’ may be used uninitialized [-Wmaybe-uninitialized]
  663 |         p.set_index(line->index(),Data()->hyperplaneindex(dot(min).second));
      |                                                           ~~~^~~~~
oja_geometry.cpp:572:13: note: ‘min’ was declared here
  572 |         int min;
      |             ^~~
g++-16 -std=gnu++20 -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 oja_iterator.cpp -o oja_iterator.o
gcc-16 -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 -Wstrict-prototypes -pedantic -mtune=native  -c ojasr.c -o ojasr.o
g++-16 -std=gnu++20 -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 point.cpp -o point.o
g++-16 -std=gnu++20 -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 random.cpp -o random.o
gcc-16 -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 -Wstrict-prototypes -pedantic -mtune=native  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++-16 -std=gnu++20 -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 simplex.cpp -o simplex.o
g++-16 -std=gnu++20 -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 stdafx.cpp -o stdafx.o
g++-16 -std=gnu++20 -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 vkm.cpp -o vkm.o
g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o OjaNP.so Matrix2D.o SubsetGenerator.o _Vector.o algorithms.o bounded_search.o data.o det.o global.o hyperplane.o index.o interface.o lattice.o line.o matrix_wrapper.o misc.o oja_data.o oja_geometry.o oja_iterator.o ojasr.o point.o random.o registerDynamicSymbol.o simplex.o stdafx.o vkm.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -latomic_asneeded -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOQHxuC/R.INSTALL35e7ae4c9f372f/OjaNP/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOQHxuC/R.INSTALL35e7ae4c9f372f/OjaNP/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOQHxuC/R.INSTALL35e7ae4c9f372f/OjaNP/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-OjaNP/00new/OjaNP/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘OjaNP’
    finding HTML links ... done
    OjaNP-package                           html  
    biochem                                 html  
    hyperplane                              html  
    oja1sampleTest                          html  
    ojaCsampleTest                          html  
    ojaMedian                               html  
    ojaMedianControl                        html  
    ojaMedianFn                             html  
    ojaRCM                                  html  
    ojaRank                                 html  
    ojaSCM                                  html  
    ojaSign                                 html  
    ojaSignedRank                           html  
** building package indices
** 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 (OjaNP)