Install log for 'BayesMallowsSMC2'

* installing *source* package ‘BayesMallowsSMC2’ ...
** this is package ‘BayesMallowsSMC2’ version ‘0.2.0’
** package ‘BayesMallowsSMC2’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BayesMallowsSMC2/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c all_topological_sorts.cpp -o all_topological_sorts.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c data.cpp -o data.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c distances.cpp -o distances.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c misc.cpp -o misc.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c options.cpp -o options.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c parameter_tracer.cpp -o parameter_tracer.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c particle.cpp -o particle.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c partition_functions.cpp -o partition_functions.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c prior.cpp -o prior.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c progress_reporter.cpp -o progress_reporter.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c rejuvenate.cpp -o rejuvenate.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c resampler.cpp -o resampler.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c run_smc.cpp -o run_smc.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_BOUNDS_CHECK -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I/usr/local/include   -fopenmp -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c sample_latent_rankings.cpp -o sample_latent_rankings.o
resampler.cpp: In function ‘arma::ivec stratsys(int, arma::vec, bool)’:
resampler.cpp:31:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   31 |   for(size_t i{}; i < n_samples; i++) u(i) = (i + rn(i)) / n_samples;
      |                   ~~^~~~~~~~~~~
all_topological_sorts.cpp: In member function ‘void Graph::alltopologicalSortUtil(std::vector<int, std::allocator<int> >&, std::vector<bool>&, long long int&, std::vector<arma::Col<int> >&, double)’:
all_topological_sorts.cpp:40:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   40 |   for (size_t i{}; i < n_items; i++) {
      |                    ~~^~~~~~~~~
rejuvenate.cpp: In member function ‘bool Particle::rejuvenate(unsigned int, const Options&, const Prior&, const std::unique_ptr<Data>&, const std::unique_ptr<PartitionFunction>&, const std::unique_ptr<Distance>&, const std::unique_ptr<Resampler>&, const arma::vec&)’:
rejuvenate.cpp:66:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   66 |   for(size_t cluster{}; cluster < prior.n_clusters; cluster++) {
      |                         ~~~~~~~~^~~~~~~~~~~~~~~~~~
rejuvenate.cpp:104:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  104 |     for(size_t cluster{}; cluster < prior.n_clusters; cluster++) {
      |                           ~~~~~~~~^~~~~~~~~~~~~~~~~~
data.cpp: In constructor ‘Rankings::Rankings(const Rcpp::List&, bool)’:
data.cpp:24:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   24 |     for(size_t i{}; i < nm.size(); i++) {
      |                     ~~^~~~~~~~~~~
data.cpp: In constructor ‘PairwisePreferences::PairwisePreferences(const Rcpp::List&, const Rcpp::List&, const Rcpp::List&)’:
data.cpp:60:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   60 |     for(size_t i{}; i < nm.size(); i++) {
      |                     ~~^~~~~~~~~~~
particle.cpp: In member function ‘void Particle::run_particle_filter(unsigned int, const Prior&, const std::unique_ptr<Data>&, const std::unique_ptr<PartitionFunction>&, const std::unique_ptr<Distance>&, const std::unique_ptr<Resampler>&, std::string, bool)’:
particle.cpp:66:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   66 |       for(size_t c{}; c < prior.n_clusters; c++) {
      |                       ~~^~~~~~~~~~~~~~~~~~
data.cpp:77:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   77 |     for(size_t i{}; i < nm.size(); i++) {
      |                     ~~^~~~~~~~~~~
data.cpp:88:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
   88 |     for(size_t i{}; i < nm.size(); i++) {
      |                     ~~^~~~~~~~~~~
particle.cpp: In function ‘double compute_log_Z(const std::vector<ParticleFilter>&, int)’:
particle.cpp:161:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  161 |   for(size_t s{}; s < max_time + 1; s++) {
      |                   ~~^~~~~~~~~~~~~~
run_smc.cpp: In function ‘Rcpp::List run_smc(Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List, Rcpp::List)’:
run_smc.cpp:44:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   44 |   for(size_t t{}; t < T; t++) {
      |                   ~~^~~
partition_functions.cpp: In member function ‘virtual double Cayley::logz(double)’:
partition_functions.cpp:25:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
   25 |   for(int i{1}; i < n_items; ++i){
      |                 ~~^~~~~~~~~
partition_functions.cpp: In member function ‘virtual double Hamming::logz(double)’:
partition_functions.cpp:35:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   35 |   for(int i{}; i < (n_items + 1); ++i){
      |                ~~^~~~~~~~~~~~~~~
partition_functions.cpp: In member function ‘virtual double Kendall::logz(double)’:
partition_functions.cpp:46:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   46 |   for(int i{1}; i < (n_items + 1); ++i){
      |                 ~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o BayesMallowsSMC2.so RcppExports.o all_topological_sorts.o data.o distances.o misc.o options.o parameter_tracer.o particle.o partition_functions.o prior.o progress_reporter.o rejuvenate.o resampler.o run_smc.o sample_latent_rankings.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BayesMallowsSMC2/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BayesMallowsSMC2/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BayesMallowsSMC2/src'
installing to /data/gannet/ripley/R/packages/tests-devel/BayesMallowsSMC2.Rcheck/00LOCK-BayesMallowsSMC2/00new/BayesMallowsSMC2/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (BayesMallowsSMC2)