* installing *source* package ‘jSDM’ ... ** package ‘jSDM’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘clang version 18.1.2’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/jSDM/src' /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit.cpp -o Rcpp_jSDM_binomial_logit.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_fixed_site.cpp -o Rcpp_jSDM_binomial_logit_fixed_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_fixed_site_lv.cpp -o Rcpp_jSDM_binomial_logit_fixed_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_lv.cpp -o Rcpp_jSDM_binomial_logit_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_rand_site.cpp -o Rcpp_jSDM_binomial_logit_rand_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_rand_site_lv.cpp -o Rcpp_jSDM_binomial_logit_rand_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_traits.cpp -o Rcpp_jSDM_binomial_logit_traits.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_traits_fixed_site.cpp -o Rcpp_jSDM_binomial_logit_traits_fixed_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_traits_fixed_site_lv.cpp -o Rcpp_jSDM_binomial_logit_traits_fixed_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_traits_lv.cpp -o Rcpp_jSDM_binomial_logit_traits_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_traits_rand_site.cpp -o Rcpp_jSDM_binomial_logit_traits_rand_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_logit_traits_rand_site_lv.cpp -o Rcpp_jSDM_binomial_logit_traits_rand_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit.cpp -o Rcpp_jSDM_binomial_probit.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_fixed_site.cpp -o Rcpp_jSDM_binomial_probit_fixed_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_fixed_site_long_format.cpp -o Rcpp_jSDM_binomial_probit_fixed_site_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_fixed_site_lv.cpp -o Rcpp_jSDM_binomial_probit_fixed_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_fixed_site_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_fixed_site_lv_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_long_format.cpp -o Rcpp_jSDM_binomial_probit_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_lv.cpp -o Rcpp_jSDM_binomial_probit_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_lv_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_rand_site.cpp -o Rcpp_jSDM_binomial_probit_rand_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_rand_site_long_format.cpp -o Rcpp_jSDM_binomial_probit_rand_site_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_rand_site_lv.cpp -o Rcpp_jSDM_binomial_probit_rand_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_rand_site_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_rand_site_lv_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits.cpp -o Rcpp_jSDM_binomial_probit_traits.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_fixed_site.cpp -o Rcpp_jSDM_binomial_probit_traits_fixed_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_fixed_site_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_fixed_site_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_fixed_site_lv.cpp -o Rcpp_jSDM_binomial_probit_traits_fixed_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_fixed_site_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_fixed_site_lv_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_lv.cpp -o Rcpp_jSDM_binomial_probit_traits_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_lv_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_rand_site.cpp -o Rcpp_jSDM_binomial_probit_traits_rand_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_rand_site_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_rand_site_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_rand_site_lv.cpp -o Rcpp_jSDM_binomial_probit_traits_rand_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_binomial_probit_traits_rand_site_lv_long_format.cpp -o Rcpp_jSDM_binomial_probit_traits_rand_site_lv_long_format.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian.cpp -o Rcpp_jSDM_gaussian.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_fixed_site.cpp -o Rcpp_jSDM_gaussian_fixed_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_fixed_site_lv.cpp -o Rcpp_jSDM_gaussian_fixed_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_lv.cpp -o Rcpp_jSDM_gaussian_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_rand_site.cpp -o Rcpp_jSDM_gaussian_rand_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_rand_site_lv.cpp -o Rcpp_jSDM_gaussian_rand_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_traits.cpp -o Rcpp_jSDM_gaussian_traits.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_traits_fixed_site.cpp -o Rcpp_jSDM_gaussian_traits_fixed_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_traits_fixed_site_lv.cpp -o Rcpp_jSDM_gaussian_traits_fixed_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_traits_lv.cpp -o Rcpp_jSDM_gaussian_traits_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_traits_rand_site.cpp -o Rcpp_jSDM_gaussian_traits_rand_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_gaussian_traits_rand_site_lv.cpp -o Rcpp_jSDM_gaussian_traits_rand_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log.cpp -o Rcpp_jSDM_poisson_log.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_fixed_site.cpp -o Rcpp_jSDM_poisson_log_fixed_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_fixed_site_lv.cpp -o Rcpp_jSDM_poisson_log_fixed_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_lv.cpp -o Rcpp_jSDM_poisson_log_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_rand_site.cpp -o Rcpp_jSDM_poisson_log_rand_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_rand_site_lv.cpp -o Rcpp_jSDM_poisson_log_rand_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_traits.cpp -o Rcpp_jSDM_poisson_log_traits.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_traits_fixed_site.cpp -o Rcpp_jSDM_poisson_log_traits_fixed_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_traits_fixed_site_lv.cpp -o Rcpp_jSDM_poisson_log_traits_fixed_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_traits_lv.cpp -o Rcpp_jSDM_poisson_log_traits_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_traits_rand_site.cpp -o Rcpp_jSDM_poisson_log_traits_rand_site.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_poisson_log_traits_rand_site_lv.cpp -o Rcpp_jSDM_poisson_log_traits_rand_site_lv.o /usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG `gsl-config --cflags` -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-clang/RcppGSL/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Rcpp_jSDM_useful.cpp -o Rcpp_jSDM_useful.o /usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -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 -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/jSDM/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/jSDM/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/jSDM/src' installing to /data/gannet/ripley/R/packages/tests-clang/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)