* installing *source* package ‘meshed’ ...
** this is package ‘meshed’ version ‘0.2.3’
** package ‘meshed’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++11
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/meshed/src'
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 covariance_lmc.cpp -o covariance_lmc.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 matern.cpp -o matern.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 mcmc_hmc_nodes.cpp -o mcmc_hmc_nodes.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 mesh_dep.cpp -o mesh_dep.o
mcmc_hmc_nodes.cpp: In member function ‘arma::vec NodeDataW::compute_dens_and_grad(double&, const arma::mat&)’:
mcmc_hmc_nodes.cpp:230:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  230 |   for(int i=0; i<nr; i++){
      |                ~^~~
mcmc_hmc_nodes.cpp: In member function ‘arma::mat NodeDataW::compute_dens_grad_neghess(double&, arma::vec&, const arma::mat&)’:
mcmc_hmc_nodes.cpp:473:36: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  473 |           for(unsigned int jx=0; jx<k; jx++){
      |                                  ~~^~
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed.cpp -o meshed.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_beta_sampler.cpp -o meshed_beta_sampler.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_betalambdatau_sampler.cpp -o meshed_betalambdatau_sampler.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_casc.cpp -o meshed_casc.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_lambda_sampler.cpp -o meshed_lambda_sampler.o
meshed_casc.cpp: In function ‘Rcpp::List meshed_casc(const arma::mat&, const arma::uvec&, int, const arma::mat&, const arma::mat&, const arma::field<arma::Col<long long unsigned int> >&, const arma::field<arma::Col<long long unsigned int> >&, const arma::vec&, const arma::vec&, const arma::field<arma::Col<long long unsigned int> >&, const arma::field<arma::Col<long long unsigned int> >&, const arma::mat&, int, const arma::mat&, const arma::mat&, const arma::umat&, const arma::field<arma::Mat<double> >&, const arma::mat&, const arma::mat&, int, int, bool, bool, bool, bool, bool, int, bool, bool)’:
meshed_casc.cpp:72:7: warning: unused variable ‘d’ [-Wunused-variable]
   72 |   int d = coords.n_cols;
      |       ^
meshed_casc.cpp:92:8: warning: variable ‘acceptable’ set but not used [-Wunused-but-set-variable]
   92 |   bool acceptable=true;
      |        ^~~~~~~~~~
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_mcmc.cpp -o meshed_mcmc.o
meshed_mcmc.cpp: In function ‘Rcpp::List meshed_mcmc(const arma::mat&, const arma::uvec&, const arma::mat&, const arma::mat&, int, const arma::field<arma::Col<long long unsigned int> >&, const arma::field<arma::Col<long long unsigned int> >&, const arma::vec&, const arma::vec&, const arma::field<arma::Col<long long unsigned int> >&, const arma::field<arma::Col<long long unsigned int> >&, const arma::mat&, const arma::mat&, const arma::vec&, const arma::vec&, int, const arma::mat&, const arma::mat&, const arma::umat&, const arma::mat&, const arma::mat&, const arma::vec&, const arma::mat&, int, int, int, int, int, int, bool, bool, bool, bool, bool, bool, int, bool, bool, bool, bool, bool, bool)’:
meshed_mcmc.cpp:172:8: warning: variable ‘acceptable’ set but not used [-Wunused-but-set-variable]
  172 |   bool acceptable = false;
      |        ^~~~~~~~~~
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_predict.cpp -o meshed_predict.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_prior_sample.cpp -o meshed_prior_sample.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_tausq_sampler.cpp -o meshed_tausq_sampler.o
meshed_tausq_sampler.cpp:69:77: warning: ‘/*’ within comment [-Wcomment]
   69 |       arma::accu(alter_data.loglik_w_comps) + arma::accu(alter_data.ll_y); //***
meshed_tausq_sampler.cpp:71:77: warning: ‘/*’ within comment [-Wcomment]
   71 |       arma::accu(param_data.loglik_w_comps) + arma::accu(param_data.ll_y); //***
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_theta_sampler.cpp -o meshed_theta_sampler.o
meshed_theta_sampler.cpp: In member function ‘void Meshed::metrop_theta()’:
meshed_theta_sampler.cpp:56:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
   56 |       for(int i=0; i<param_data.theta.n_rows-2; i++){
      |                    ~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_w_prior_sampler.cpp -o meshed_w_prior_sampler.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 meshed_w_sampler.cpp -o meshed_w_sampler.o
meshed_w_sampler.cpp: In member function ‘void Meshed::nongaussian_w(MeshDataLMC&, bool)’:
meshed_w_sampler.cpp:310:14: warning: unused variable ‘do_gibbs’ [-Wunused-variable]
  310 |         bool do_gibbs = arma::all(familyid == 0);
      |              ^~~~~~~~
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 postprocess.cpp -o postprocess.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 utils_caching.cpp -o utils_caching.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 utils_check_groups.cpp -o utils_check_groups.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 utils_find_nan.cpp -o utils_find_nan.o
g++ -std=gnu++11 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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 utils_irls.cpp -o utils_irls.o
g++ -std=gnu++11 -shared -L/usr/local/lib64 -o meshed.so RcppExports.o covariance_lmc.o matern.o mcmc_hmc_nodes.o mesh_dep.o meshed.o meshed_beta_sampler.o meshed_betalambdatau_sampler.o meshed_casc.o meshed_lambda_sampler.o meshed_mcmc.o meshed_predict.o meshed_prior_sample.o meshed_tausq_sampler.o meshed_theta_sampler.o meshed_w_prior_sampler.o meshed_w_sampler.o postprocess.o utils_caching.o utils_check_groups.o utils_find_nan.o utils_irls.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/meshed/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/meshed/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/meshed/src'
installing to /data/gannet/ripley/R/packages/tests-devel/meshed.Rcheck/00LOCK-meshed/00new/meshed/libs
** R
** 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 (meshed)