* installing *source* package ‘ACEt’ ...
** package ‘ACEt’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (GCC) 13.2.0’
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ACEt/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c AtCtEt.cpp -o AtCtEt.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c AtCtEtp.cpp -o AtCtEtp.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c AtDtEt.cpp -o AtDtEt.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c AtEtp.cpp -o AtEtp.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RInterface.cc -o RInterface.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c mcmc.cc -o mcmc.o
gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/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 packagename_init.c -o packagename_init.o
AtCtEtp.cpp: In function 'SEXPREC* loglik_AtCtEt_epsp_g_c(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
AtCtEtp.cpp:294:13: warning: unused variable 'num_a' [-Wunused-variable]
294 | int num_a = b_a_m.n_cols;
| ^~~~~
AtCtEtp.cpp:295:13: warning: unused variable 'num_c' [-Wunused-variable]
295 | int num_c = b_c_m.n_cols;
| ^~~~~
AtCtEtp.cpp:296:13: warning: unused variable 'num_e' [-Wunused-variable]
296 | int num_e = b_e_m.n_cols;
| ^~~~~
mcmc.cc: In function 'void ci_mh_atctet(double*, int*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, double*)':
mcmc.cc:31:83: warning: typedef 'gen_type' locally defined but not used [-Wunused-local-typedefs]
31 | typedef boost::variate_generator<base_generator_type&, distribution_type> gen_type;
| ^~~~~~~~
mcmc.cc:33:84: warning: typedef 'gen_type3' locally defined but not used [-Wunused-local-typedefs]
33 | typedef boost::variate_generator<base_generator_type&, distribution_type3> gen_type3;
| ^~~~~~~~~
mcmc.cc: In function 'void ci_mh_atctet_2(double*, int*, int*, int*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, int*, double*)':
mcmc.cc:925:36: warning: typedef 'Mat_i' locally defined but not used [-Wunused-local-typedefs]
925 | typedef std::vector<Vec_i> Mat_i;
| ^~~~~
mcmc.cc:932:83: warning: typedef 'gen_type' locally defined but not used [-Wunused-local-typedefs]
932 | typedef boost::variate_generator<base_generator_type&, distribution_type> gen_type;
| ^~~~~~~~
mcmc.cc:934:84: warning: typedef 'gen_type3' locally defined but not used [-Wunused-local-typedefs]
934 | typedef boost::variate_generator<base_generator_type&, distribution_type3> gen_type3;
| ^~~~~~~~~
AtDtEt.cpp: In function 'SEXPREC* hessian_AtDtEt_esp_c(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
AtDtEt.cpp:542:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
542 | for(int i=0; i<num_t; i++)
| ^~~
AtDtEt.cpp:549:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
549 | return(Rcpp::wrap(res));
| ^~~~~~
AtEtp.cpp: In function 'SEXPREC* loglik_AtEt_epsp_g_c(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
AtEtp.cpp:212:13: warning: unused variable 'num_a' [-Wunused-variable]
212 | int num_a = b_a_m.n_cols;
| ^~~~~
AtEtp.cpp:213:13: warning: unused variable 'num_e' [-Wunused-variable]
213 | int num_e = b_e_m.n_cols;
| ^~~~~
g++-13 -std=gnu++17 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o ACEt.so AtCtEt.o AtCtEtp.o AtDtEt.o AtEtp.o RInterface.o mcmc.o packagename_init.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ACEt/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/ACEt/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/ACEt/src'
installing to /data/gannet/ripley/R/packages/tests-devel/ACEt.Rcheck/00LOCK-ACEt/00new/ACEt/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 (ACEt)