* installing *source* package ‘pumBayes’ ...
** this is package ‘pumBayes’ version ‘1.0.0’
** package ‘pumBayes’ 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)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/pumBayes/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppDist/include' -I'/data/gannet/ripley/R/test-dev/mvtnorm/include' -I'/data/gannet/ripley/R/test-dev/RcppTN/include' -I/usr/local/include -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 -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppDist/include' -I'/data/gannet/ripley/R/test-dev/mvtnorm/include' -I'/data/gannet/ripley/R/test-dev/RcppTN/include' -I/usr/local/include -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 rtn1.cpp -o rtn1.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppDist/include' -I'/data/gannet/ripley/R/test-dev/mvtnorm/include' -I'/data/gannet/ripley/R/test-dev/RcppTN/include' -I/usr/local/include -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 three_utility_probit_helper_functions.cpp -o three_utility_probit_helper_functions.o
three_utility_probit_helper_functions.cpp: In function ‘Rcpp::List sample_probit_static_rcpp(arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, int, int, int, int, int, double, double, arma::vec, arma::mat, arma::vec, arma::mat, double, int, int, int, double, int, bool)’:
three_utility_probit_helper_functions.cpp:571:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
571 | if (!is_finite(vote_m(k, j))) {
| ~~~~~~~~~^~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo:518,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
from three_utility_probit_helper_functions.cpp:1:
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
three_utility_probit_helper_functions.cpp: In function ‘Rcpp::List sample_probit_dynamic_rcpp_flip(arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::uvec, arma::uvec, arma::uvec, arma::umat, arma::uvec, int, int, int, int, int, arma::vec, arma::mat, arma::vec, arma::mat, double, double, double, double, int, int, int, double, arma::uvec, arma::uvec, arma::uvec, arma::uvec, bool)’:
three_utility_probit_helper_functions.cpp:819:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
819 | if (!is_finite(vote_m(j, k))) {
| ~~~~~~~~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
three_utility_probit_helper_functions.cpp: In function ‘arma::vec calc_waic_probit_bggum_three_utility(arma::mat, arma::mat, arma::mat, arma::mat, int)’:
three_utility_probit_helper_functions.cpp:1115:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
1115 | if (!is_finite(case_vote_m(i, j))) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
three_utility_probit_helper_functions.cpp: In function ‘arma::vec calc_waic_probit_bggum_three_utility_block_rcpp(arma::mat, arma::mat, arma::mat, arma::mat, arma::uvec, arma::mat)’:
three_utility_probit_helper_functions.cpp:1163:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
1163 | if (!is_finite(case_vote_m(i, j))) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
three_utility_probit_helper_functions.cpp: In function ‘arma::vec calc_waic_probit_bggum_three_utility_block_vote_rcpp(arma::mat, arma::mat, arma::mat, arma::mat, arma::mat)’:
three_utility_probit_helper_functions.cpp:1207:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
1207 | if (!is_finite(case_vote_m(i, j))) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
three_utility_probit_helper_functions.cpp: In function ‘arma::vec calc_waic_cpp(arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::mat)’:
three_utility_probit_helper_functions.cpp:1249:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
1249 | if (!is_finite(case_vote_m(ind, j))) {
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
three_utility_probit_helper_functions.cpp: In function ‘Rcpp::List sample_probit_dynamic_rcpp(arma::mat, arma::mat, arma::mat, arma::mat, arma::mat, arma::uvec, arma::uvec, arma::uvec, arma::umat, arma::uvec, int, int, int, int, int, arma::vec, arma::mat, arma::vec, arma::mat, double, double, double, double, int, int, int, double, arma::uvec, arma::uvec, arma::uvec, arma::uvec, bool)’:
three_utility_probit_helper_functions.cpp:1518:23: warning: ‘bool arma::is_finite(eT, const typename arma_scalar_only<T>::result*) [with eT = double; typename arma_scalar_only<T>::result = double]’ is deprecated: change arma::is_finite(val) to std::isfinite(val) [-Wdeprecated-declarations]
1518 | if (!is_finite(vote_m(j, k))) {
| ~~~~~~~~~^~~~~~~~~~~~~~
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:167:1: note: declared here
167 | is_finite(const eT x, const typename arma_scalar_only<eT>::result* junk = nullptr)
| ^~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o pumBayes.so RcppExports.o rtn1.o three_utility_probit_helper_functions.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/pumBayes/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/pumBayes/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/pumBayes/src'
installing to /data/gannet/ripley/R/packages/tests-devel/pumBayes.Rcheck/00LOCK-pumBayes/00new/pumBayes/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (pumBayes)