* installing *source* package ‘jSDM’ ... ** this is package ‘jSDM’ version ‘0.2.6’ ** package ‘jSDM’ 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/jSDM/src' g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit.cpp -o Rcpp_jSDM_binomial_logit.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_fixed_site.cpp -o Rcpp_jSDM_binomial_logit_fixed_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_fixed_site_lv.cpp -o Rcpp_jSDM_binomial_logit_fixed_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_lv.cpp -o Rcpp_jSDM_binomial_logit_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_rand_site.cpp -o Rcpp_jSDM_binomial_logit_rand_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_rand_site_lv.cpp -o Rcpp_jSDM_binomial_logit_rand_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_traits.cpp -o Rcpp_jSDM_binomial_logit_traits.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_traits_fixed_site.cpp -o Rcpp_jSDM_binomial_logit_traits_fixed_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_traits_fixed_site_lv.cpp -o Rcpp_jSDM_binomial_logit_traits_fixed_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_traits_lv.cpp -o Rcpp_jSDM_binomial_logit_traits_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_traits_rand_site.cpp -o Rcpp_jSDM_binomial_logit_traits_rand_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_logit_traits_rand_site_lv.cpp -o Rcpp_jSDM_binomial_logit_traits_rand_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit.cpp -o Rcpp_jSDM_binomial_probit.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_fixed_site.cpp -o Rcpp_jSDM_binomial_probit_fixed_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_fixed_site_long_format.cpp -o Rcpp_jSDM_binomial_probit_fixed_site_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_fixed_site_lv.cpp -o Rcpp_jSDM_binomial_probit_fixed_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_fixed_site_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_fixed_site_lv_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_long_format.cpp -o Rcpp_jSDM_binomial_probit_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_lv.cpp -o Rcpp_jSDM_binomial_probit_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_lv_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_rand_site.cpp -o Rcpp_jSDM_binomial_probit_rand_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_rand_site_long_format.cpp -o Rcpp_jSDM_binomial_probit_rand_site_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_rand_site_lv.cpp -o Rcpp_jSDM_binomial_probit_rand_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_rand_site_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_rand_site_lv_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits.cpp -o Rcpp_jSDM_binomial_probit_traits.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_fixed_site.cpp -o Rcpp_jSDM_binomial_probit_traits_fixed_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_fixed_site_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_fixed_site_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_fixed_site_lv.cpp -o Rcpp_jSDM_binomial_probit_traits_fixed_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_fixed_site_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_fixed_site_lv_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_lv.cpp -o Rcpp_jSDM_binomial_probit_traits_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_lv_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_rand_site.cpp -o Rcpp_jSDM_binomial_probit_traits_rand_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_rand_site_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_rand_site_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_rand_site_lv.cpp -o Rcpp_jSDM_binomial_probit_traits_rand_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_binomial_probit_traits_rand_site_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_rand_site_lv_long_format.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian.cpp -o Rcpp_jSDM_gaussian.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_fixed_site.cpp -o Rcpp_jSDM_gaussian_fixed_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_fixed_site_lv.cpp -o Rcpp_jSDM_gaussian_fixed_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_lv.cpp -o Rcpp_jSDM_gaussian_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_rand_site.cpp -o Rcpp_jSDM_gaussian_rand_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_rand_site_lv.cpp -o Rcpp_jSDM_gaussian_rand_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_traits.cpp -o Rcpp_jSDM_gaussian_traits.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_traits_fixed_site.cpp -o Rcpp_jSDM_gaussian_traits_fixed_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_traits_fixed_site_lv.cpp -o Rcpp_jSDM_gaussian_traits_fixed_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_traits_lv.cpp -o Rcpp_jSDM_gaussian_traits_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_traits_rand_site.cpp -o Rcpp_jSDM_gaussian_traits_rand_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_gaussian_traits_rand_site_lv.cpp -o Rcpp_jSDM_gaussian_traits_rand_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log.cpp -o Rcpp_jSDM_poisson_log.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_fixed_site.cpp -o Rcpp_jSDM_poisson_log_fixed_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_fixed_site_lv.cpp -o Rcpp_jSDM_poisson_log_fixed_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_lv.cpp -o Rcpp_jSDM_poisson_log_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_rand_site.cpp -o Rcpp_jSDM_poisson_log_rand_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_rand_site_lv.cpp -o Rcpp_jSDM_poisson_log_rand_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_traits.cpp -o Rcpp_jSDM_poisson_log_traits.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_traits_fixed_site.cpp -o Rcpp_jSDM_poisson_log_traits_fixed_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_traits_fixed_site_lv.cpp -o Rcpp_jSDM_poisson_log_traits_fixed_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_traits_lv.cpp -o Rcpp_jSDM_poisson_log_traits_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_traits_rand_site.cpp -o Rcpp_jSDM_poisson_log_traits_rand_site.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_poisson_log_traits_rand_site_lv.cpp -o Rcpp_jSDM_poisson_log_traits_rand_site_lv.o g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG `gsl-config --cflags` -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/RcppGSL/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 Rcpp_jSDM_useful.cpp -o Rcpp_jSDM_useful.o Rcpp_jSDM_useful.cpp: In function ‘double betadens_logit(double, void*)’: Rcpp_jSDM_useful.cpp:85:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 85 | if(arma::is_finite(d->alpha_run)){ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 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 Rcpp_jSDM_useful.cpp:8: /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ Rcpp_jSDM_useful.cpp: In function ‘double lambdadens_logit(double, void*)’: Rcpp_jSDM_useful.cpp:120:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 120 | if(arma::is_finite(d->alpha_run)){ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ Rcpp_jSDM_useful.cpp: In function ‘double lambdaUdens_logit(double, void*)’: Rcpp_jSDM_useful.cpp:154:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 154 | if(arma::is_finite(d->alpha_run)){ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ Rcpp_jSDM_useful.cpp: In function ‘double Wdens_logit(double, void*)’: Rcpp_jSDM_useful.cpp:220:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 220 | if(arma::is_finite(d->alpha_run)){ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ Rcpp_jSDM_useful.cpp: In function ‘double betadens_pois(double, void*)’: Rcpp_jSDM_useful.cpp:257:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 257 | if(arma::is_finite(d->alpha_run)){ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ Rcpp_jSDM_useful.cpp: In function ‘double lambdadens_pois(double, void*)’: Rcpp_jSDM_useful.cpp:292:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 292 | if(arma::is_finite(d->alpha_run)){ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ Rcpp_jSDM_useful.cpp: In function ‘double lambdaUdens_pois(double, void*)’: Rcpp_jSDM_useful.cpp:326:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 326 | if(arma::is_finite(d->alpha_run)){ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ Rcpp_jSDM_useful.cpp: In function ‘double Wdens_pois(double, void*)’: Rcpp_jSDM_useful.cpp:392:23: warning: ‘bool arma::is_finite(const Base<typename T1::elem_type, T1>&) [with T1 = Mat<double>; typename T1::elem_type = double]’ is deprecated: change arma::is_finite(X) to X.is_finite() [-Wdeprecated-declarations] 392 | if(arma::is_finite(d->alpha_run)){ | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/fn_misc.hpp:181:1: note: declared here 181 | is_finite(const Base<typename T1::elem_type,T1>& X) | ^~~~~~~~~ g++ -std=gnu++17 -shared -L/usr/local/lib64 -o jSDM.so RcppExports.o Rcpp_jSDM_binomial_logit.o Rcpp_jSDM_binomial_logit_fixed_site.o Rcpp_jSDM_binomial_logit_fixed_site_lv.o Rcpp_jSDM_binomial_logit_lv.o Rcpp_jSDM_binomial_logit_rand_site.o Rcpp_jSDM_binomial_logit_rand_site_lv.o Rcpp_jSDM_binomial_logit_traits.o Rcpp_jSDM_binomial_logit_traits_fixed_site.o Rcpp_jSDM_binomial_logit_traits_fixed_site_lv.o Rcpp_jSDM_binomial_logit_traits_lv.o Rcpp_jSDM_binomial_logit_traits_rand_site.o Rcpp_jSDM_binomial_logit_traits_rand_site_lv.o Rcpp_jSDM_binomial_probit.o Rcpp_jSDM_binomial_probit_fixed_site.o Rcpp_jSDM_binomial_probit_fixed_site_long_format.o Rcpp_jSDM_binomial_probit_fixed_site_lv.o Rcpp_jSDM_binomial_probit_fixed_site_lv_long_format.o Rcpp_jSDM_binomial_probit_long_format.o Rcpp_jSDM_binomial_probit_lv.o Rcpp_jSDM_binomial_probit_lv_long_format.o Rcpp_jSDM_binomial_probit_rand_site.o Rcpp_jSDM_binomial_probit_rand_site_long_format.o Rcpp_jSDM_binomial_probit_rand_site_lv.o Rcpp_jSDM_binomial_probit_rand_site_lv_long_format.o Rcpp_jSDM_binomial_probit_traits.o Rcpp_jSDM_binomial_probit_traits_fixed_site.o Rcpp_jSDM_binomial_probit_traits_fixed_site_long_format.o Rcpp_jSDM_binomial_probit_traits_fixed_site_lv.o Rcpp_jSDM_binomial_probit_traits_fixed_site_lv_long_format.o Rcpp_jSDM_binomial_probit_traits_long_format.o Rcpp_jSDM_binomial_probit_traits_lv.o Rcpp_jSDM_binomial_probit_traits_lv_long_format.o Rcpp_jSDM_binomial_probit_traits_rand_site.o Rcpp_jSDM_binomial_probit_traits_rand_site_long_format.o Rcpp_jSDM_binomial_probit_traits_rand_site_lv.o Rcpp_jSDM_binomial_probit_traits_rand_site_lv_long_format.o Rcpp_jSDM_gaussian.o Rcpp_jSDM_gaussian_fixed_site.o Rcpp_jSDM_gaussian_fixed_site_lv.o Rcpp_jSDM_gaussian_lv.o Rcpp_jSDM_gaussian_rand_site.o Rcpp_jSDM_gaussian_rand_site_lv.o Rcpp_jSDM_gaussian_traits.o Rcpp_jSDM_gaussian_traits_fixed_site.o Rcpp_jSDM_gaussian_traits_fixed_site_lv.o Rcpp_jSDM_gaussian_traits_lv.o Rcpp_jSDM_gaussian_traits_rand_site.o Rcpp_jSDM_gaussian_traits_rand_site_lv.o Rcpp_jSDM_poisson_log.o Rcpp_jSDM_poisson_log_fixed_site.o Rcpp_jSDM_poisson_log_fixed_site_lv.o Rcpp_jSDM_poisson_log_lv.o Rcpp_jSDM_poisson_log_rand_site.o Rcpp_jSDM_poisson_log_rand_site_lv.o Rcpp_jSDM_poisson_log_traits.o Rcpp_jSDM_poisson_log_traits_fixed_site.o Rcpp_jSDM_poisson_log_traits_fixed_site_lv.o Rcpp_jSDM_poisson_log_traits_lv.o Rcpp_jSDM_poisson_log_traits_rand_site.o Rcpp_jSDM_poisson_log_traits_rand_site_lv.o Rcpp_jSDM_useful.o -lgsl -lgslcblas -lm -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/jSDM/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/jSDM/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/jSDM/src' installing to /data/gannet/ripley/R/packages/tests-devel/jSDM.Rcheck/00LOCK-jSDM/00new/jSDM/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (jSDM)