* installing *source* package ‘BHSBVAR’ ... ** this is package ‘BHSBVAR’ version ‘3.1.2’ ** package ‘BHSBVAR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’ 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/BHSBVAR/src' gcc -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/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c BHSBVAR-init.c -o BHSBVAR-init.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/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 BHSBVAR.cpp -o BHSBVAR.o BHSBVAR.cpp: In function ‘double sum_log_prior_densities(const arma::mat&, const arma::cube&, const arma::cube&, const arma::cube&)’: BHSBVAR.cpp:86:26: 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] 86 | if (arma::is_finite(pA(i, j, 0))) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ 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 BHSBVAR.cpp:8: /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) | ^~~~~~~~~ BHSBVAR.cpp:111:26: 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] 111 | if (arma::is_finite(pH(i, j, 0))) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /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) | ^~~~~~~~~ BHSBVAR.cpp:138:22: 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] 138 | if (arma::is_finite(pdetA(0, 0, 0))) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /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) | ^~~~~~~~~ BHSBVAR.cpp: In function ‘arma::mat proposal_function(const arma::mat&, const arma::cube&, const arma::cube&, const arma::cube&, const arma::mat&)’: BHSBVAR.cpp:202:27: 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] 202 | if ((arma::is_finite(pH(j, i, 0))) && (pH(j, i, 0) == 0.0) && (arma::is_finite(pH(j, i, 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) | ^~~~~~~~~ BHSBVAR.cpp:202:85: 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] 202 | if ((arma::is_finite(pH(j, i, 0))) && (pH(j, i, 0) == 0.0) && (arma::is_finite(pH(j, i, 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) | ^~~~~~~~~ BHSBVAR.cpp:229:28: 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] 229 | if (arma::is_finite(pA(j, i, 0))) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /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) | ^~~~~~~~~ BHSBVAR.cpp:233:30: 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] 233 | if (arma::is_finite(pA(j, i, 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) | ^~~~~~~~~ BHSBVAR.cpp:281:31: 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] 281 | if ((arma::is_finite(pH(j, i, 0))) && (arma::is_finite(pH(j, i, 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) | ^~~~~~~~~ BHSBVAR.cpp:281:65: 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] 281 | if ((arma::is_finite(pH(j, i, 0))) && (arma::is_finite(pH(j, i, 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) | ^~~~~~~~~ BHSBVAR.cpp:302:45: 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] 302 | if ((sign_test == 0) && (arma::is_finite(pdetA(0, 0, 0))) && (arma::is_finite(pdetA(0, 0, 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) | ^~~~~~~~~ BHSBVAR.cpp:302:82: 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] 302 | if ((sign_test == 0) && (arma::is_finite(pdetA(0, 0, 0))) && (arma::is_finite(pdetA(0, 0, 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) | ^~~~~~~~~ BHSBVAR.cpp: In function ‘arma::field<arma::Cube<double> > MH(const arma::mat&, const arma::mat&, arma::uword, const arma::mat&, const arma::mat&, const arma::cube&, const arma::cube&, const arma::cube&, const arma::mat&, const arma::mat&, const arma::cube&, const arma::mat&, arma::mat, arma::uword, arma::uword, const arma::mat&)’: BHSBVAR.cpp:368:30: 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] 368 | if (arma::is_finite(pA(j, i, 6))) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /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) | ^~~~~~~~~ BHSBVAR.cpp:402:32: 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] 402 | if (arma::is_finite(pA(j, i, 6))) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /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) | ^~~~~~~~~ BHSBVAR.cpp: In function ‘Rcpp::List den_function(const arma::cube&, const arma::cube&)’: BHSBVAR.cpp:521:26: 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] 521 | if (arma::is_finite(priors(i, j, 0))) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /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) | ^~~~~~~~~ BHSBVAR.cpp: In function ‘Rcpp::List MAIN(const arma::mat&, const arma::mat&, const arma::mat&, const arma::mat&, arma::uword, const arma::cube&, const arma::cube&, const arma::cube&, const arma::mat&, const arma::mat&, const arma::cube&, const arma::mat&, const arma::mat&, arma::uword, arma::uword, arma::uword, const arma::mat&, double)’: BHSBVAR.cpp:938:26: 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] 938 | if (arma::is_finite(pA(j, i, 6))) { | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~ /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 -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/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 -shared -L/usr/local/lib64 -o BHSBVAR.so BHSBVAR-init.o BHSBVAR.o RcppExports.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/BHSBVAR/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BHSBVAR/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BHSBVAR/src' installing to /data/gannet/ripley/R/packages/tests-devel/BHSBVAR.Rcheck/00LOCK-BHSBVAR/00new/BHSBVAR/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 (BHSBVAR)