* installing *source* package ‘stan4bart’ ...
** this is package ‘stan4bart’ version ‘0.0-10’
** package ‘stan4bart’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for x86 cpuid output... unknown
checking for x86-AVX xgetbv output... unknown
checking for x86 cpuid 0x00000000 output... d:756e6547:6c65746e:49656e69
checking for x86 cpuid 0x00000001 output... 206d7:9200800:1fbee3ff:bfebfbff
checking whether SSE2 is supported by the processor... yes
checking whether SSE2 is supported by the processor and OS... yes
checking whether C++ compiler accepts -msse2... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for malloc.h... yes
checking size of size_t... 8
checking alignment of void*... 8
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for working posix_memalign... yes
checking for ffs... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
using C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/stan4bart/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/dbarts/include' -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -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 -flto=10 -c bart_util.cpp -o bart_util.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/dbarts/include' -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -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 -flto=10 -c init.cpp -o init.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/dbarts/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 -flto=10 -c misc_adaptiveRadixTree.c -o misc_adaptiveRadixTree.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/dbarts/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 -flto=10 -c misc_string.c -o misc_string.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/dbarts/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 -flto=10 -c rc_bounds.c -o rc_bounds.o
gcc -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/dbarts/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 -flto=10 -c rc_util.c -o rc_util.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/data/gannet/ripley/R/test-dev/BH/include' -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppEigen/include' -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -I'/data/gannet/ripley/R/test-dev/dbarts/include' -I/usr/local/include -I'/data/gannet/ripley/R/test-dev/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -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 -flto=10 -c stan_sampler.cpp -o stan_sampler.o
In file included from include/stan/model/model_header.hpp:15,
from stan_files/continuous.hpp:43,
from stan_sampler.cpp:16:
include/stan/model/model_base_crtp.hpp:93:20: warning: ‘stan::math::var stan::model::model_base_crtp<M>::log_prob(Eigen::Matrix<stan::math::var_value<double>, -1, 1>&, std::ostream*) const [with M = continuous_model_namespace::continuous_model; stan::math::var = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
93 | inline math::var log_prob(Eigen::Matrix<math::var, -1, 1>& theta,
| ^~~~~~~~
stan_files/continuous.hpp:3382:15: note: by ‘T_ continuous_model_namespace::continuous_model::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const’
3382 | inline T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
| ^~~~~~~~
include/stan/model/model_base_crtp.hpp:88:17: warning: ‘double stan::model::model_base_crtp<M>::log_prob(Eigen::VectorXd&, std::ostream*) const [with M = continuous_model_namespace::continuous_model; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
88 | inline double log_prob(Eigen::VectorXd& theta,
| ^~~~~~~~
stan_files/continuous.hpp:3382:15: note: by ‘T_ continuous_model_namespace::continuous_model::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const’
3382 | inline T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
| ^~~~~~~~
include/stan/model/model_base_crtp.hpp:149:20: warning: ‘stan::math::var stan::model::model_base_crtp<M>::log_prob(std::vector<stan::math::var_value<double>, std::allocator<stan::math::var_value<double> > >&, std::vector<int>&, std::ostream*) const [with M = continuous_model_namespace::continuous_model; stan::math::var = stan::math::var_value<double>; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
149 | inline math::var log_prob(std::vector<math::var>& theta,
| ^~~~~~~~
stan_files/continuous.hpp:3382:15: note: by ‘T_ continuous_model_namespace::continuous_model::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const’
3382 | inline T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
| ^~~~~~~~
include/stan/model/model_base_crtp.hpp:144:17: warning: ‘double stan::model::model_base_crtp<M>::log_prob(std::vector<double>&, std::vector<int>&, std::ostream*) const [with M = continuous_model_namespace::continuous_model; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
144 | inline double log_prob(std::vector<double>& theta, std::vector<int>& theta_i,
| ^~~~~~~~
stan_files/continuous.hpp:3382:15: note: by ‘T_ continuous_model_namespace::continuous_model::log_prob(Eigen::Matrix<T_job_param, -1, 1>&, std::ostream*) const’
3382 | inline T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
| ^~~~~~~~
include/stan/model/model_base_crtp.hpp:133:8: warning: ‘void stan::model::model_base_crtp<M>::write_array(boost::random::ecuyer1988&, Eigen::VectorXd&, Eigen::VectorXd&, bool, bool, std::ostream*) const [with M = continuous_model_namespace::continuous_model; boost::random::ecuyer1988 = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
133 | void write_array(boost::ecuyer1988& rng, Eigen::VectorXd& theta,
| ^~~~~~~~~~~
stan_files/continuous.hpp:3338:17: note: by ‘void continuous_model_namespace::continuous_model::write_array(RNG&, Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&, bool, bool, std::ostream*) const’
3338 | inline void write_array(RNG& base_rng,
| ^~~~~~~~~~~
include/stan/model/model_base_crtp.hpp:195:8: warning: ‘void stan::model::model_base_crtp<M>::write_array(boost::random::ecuyer1988&, std::vector<double>&, std::vector<int>&, std::vector<double>&, bool, bool, std::ostream*) const [with M = continuous_model_namespace::continuous_model; boost::random::ecuyer1988 = boost::random::additive_combine_engine<boost::random::linear_congruential_engine<unsigned int, 40014, 0, 2147483563>, boost::random::linear_congruential_engine<unsigned int, 40692, 0, 2147483399> >; std::ostream = std::basic_ostream<char>]’ was hidden [-Woverloaded-virtual=]
195 | void write_array(boost::ecuyer1988& rng, std::vector<double>& theta,
| ^~~~~~~~~~~
stan_files/continuous.hpp:3338:17: note: by ‘void continuous_model_namespace::continuous_model::write_array(RNG&, Eigen::Matrix<double, -1, 1>&, Eigen::Matrix<double, -1, 1>&, bool, bool, std::ostream*) const’
3338 | inline void write_array(RNG& base_rng,
| ^~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o stan4bart.so bart_util.o init.o misc_adaptiveRadixTree.o misc_string.o rc_bounds.o rc_util.o stan_sampler.o -L/data/gannet/ripley/R/test-dev/RcppParallel/lib/ -Wl,-rpath,/data/gannet/ripley/R/test-dev/RcppParallel/lib/ -ltbb -ltbbmalloc
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/stan4bart/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/stan4bart/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/stan4bart/src'
installing to /data/gannet/ripley/R/packages/tests-devel/stan4bart.Rcheck/00LOCK-stan4bart/00new/stan4bart/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (stan4bart)