* installing *source* package ‘stpm’ ...
** package ‘stpm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 19.1.3’
using C++ compiler: ‘clang version 19.1.3’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/stpm/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c devlik.cpp -o devlik.o
devlik.cpp:459:6: warning: unused variable 't_n' [-Wunused-variable]
459 | int t_n = m0_v.n_elem;
| ^~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c devlik_g.cpp -o devlik_g.o
devlik_g.cpp:407:6: warning: unused variable 't_n' [-Wunused-variable]
407 | int t_n = m0_v.n_elem;
| ^~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c devlik_g_2.cpp -o devlik_g_2.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c hes_spm_g.cpp -o hes_spm_g.o
devlik_g_2.cpp:362:6: warning: unused variable 't_n' [-Wunused-variable]
362 | int t_n = m0_v.n_elem;
| ^~~
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c loglik.cpp -o loglik.o
loglik.cpp:26:9: warning: unused variable 'c1' [-Wunused-variable]
26 | double c1 = (u / (r0 - rs) + 2 * q)*exp(-1 * u*t0);
| ^~
loglik.cpp:42:9: warning: unused variable 'c1' [-Wunused-variable]
42 | double c1 = (u / (r0 - rs) + 2 * q)*exp((-1) * u*t0);
| ^~
loglik.cpp:43:9: warning: unused variable 'w_u' [-Wunused-variable]
43 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik.cpp:59:9: warning: unused variable 'w_u' [-Wunused-variable]
59 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik.cpp:114:6: warning: unused variable 't_n' [-Wunused-variable]
114 | int t_n = m0_v.n_elem;
| ^~~
5 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c loglik_g.cpp -o loglik_g.o
loglik_g.cpp:34:9: warning: unused variable 'c1' [-Wunused-variable]
34 | double c1 = (u / (r0 - rs) + 2 * q)*exp(-1 * u*t0);
| ^~
loglik_g.cpp:55:9: warning: unused variable 'c1' [-Wunused-variable]
55 | double c1 = (u / (r0 - rs) + 2 * q)*exp((-1) * u*t0);
| ^~
loglik_g.cpp:56:9: warning: unused variable 'w_u' [-Wunused-variable]
56 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik_g.cpp:77:9: warning: unused variable 'w_u' [-Wunused-variable]
77 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik_g.cpp:140:6: warning: unused variable 't_n' [-Wunused-variable]
140 | int t_n = m0_v.n_elem;
| ^~~
5 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c loglik_g_2.cpp -o loglik_g_2.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c simdataND.cpp -o simdataND.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spm_1D.cpp -o spm_1D.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spm_discrete.cpp -o spm_discrete.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spm_integral_MD.cpp -o spm_integral_MD.o
spm_1D.cpp:23:15: warning: variable 'hf1H' set but not used [-Wunused-but-set-variable]
23 | double hfH, hf1H, mu0Ht, mu;
| ^
spm_1D.cpp:78:9: warning: variable 'res' set but not used [-Wunused-but-set-variable]
78 | int res = func1(k1ar, t,out, fH, f1H, aH, bH, QH, thetaH);
| ^
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spm_integral_md_linear.cpp -o spm_integral_md_linear.o
/usr/local/clang19/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c stpm_init.c -o stpm_init.o
loglik_g_2.cpp:35:9: warning: unused variable 'c1' [-Wunused-variable]
35 | double c1 = (u / (r0 - rs) + 2 * q)*exp(-1 * u*t0);
| ^~
loglik_g_2.cpp:58:9: warning: unused variable 'c1' [-Wunused-variable]
58 | double c1 = (u / (r0 - rs) + 2 * q)*exp((-1) * u*t0);
| ^~
loglik_g_2.cpp:59:9: warning: unused variable 'w_u' [-Wunused-variable]
59 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik_g_2.cpp:82:9: warning: unused variable 'w_u' [-Wunused-variable]
82 | double w_u = (-1)*q*f + q*a*(f - f1) / sqrt(pow(a, 2) + 2 * q*pow(b, 2));
| ^~~
loglik_g_2.cpp:147:6: warning: unused variable 't_n' [-Wunused-variable]
147 | int t_n = m0_v.n_elem;
| ^~~
5 warnings generated.
spm_integral_MD.cpp:1050:17: warning: variable 'L1Y' set but not used [-Wunused-but-set-variable]
1050 | long double L1Y, L1Q, L0Y, L0Q;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o stpm.so devlik.o devlik_g.o devlik_g_2.o hes_spm_g.o loglik.o loglik_g.o loglik_g_2.o simdataND.o spm_1D.o spm_discrete.o spm_integral_MD.o spm_integral_md_linear.o stpm_init.o -fopenmp -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/stpm/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/stpm/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/stpm/src'
installing to /data/gannet/ripley/R/packages/tests-clang/stpm.Rcheck/00LOCK-stpm/00new/stpm/libs
** R
** data
** 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 (stpm)