* installing *source* package ‘stan4bart’ ...
** 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++-14 -std=gnu++17 accepts -g... yes
checking for g++-14 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++-14 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++-14 -std=gnu++17 accepts -g... (cached) yes
checking for g++-14 -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-14
checking whether the compiler supports GNU C... yes
checking whether gcc-14 accepts -g... yes
checking for gcc-14 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... 206d7:2200800:1fbee3ff: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-14 (GCC) 14.2.0’
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
using C++17
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/stan4bart/src'
g++-14 -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 -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c bart_util.cpp -o bart_util.o
In file included from bart_util.hpp:4,
from bart_util.cpp:1:
include/ext/Rinternals.h:30:9: warning: "R_NO_REMAP" redefined
30 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
g++-14 -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 -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c init.cpp -o init.o
In file included from init.cpp:1:
include/ext/Rinternals.h:30:9: warning: "R_NO_REMAP" redefined
30 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
gcc-14 -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 -DC99_INLINE_SEMANTICS=0 -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
In file included from include/stan/math/prim/prob/std_normal_ccdf_log.hpp:5,
from include/stan/math/prim/prob.hpp:328,
from include/stan/math/prim.hpp:16,
from include/stan/io/dump.hpp:7,
from stan_sampler_includes.hpp:78,
from stan_sampler.hpp:15,
from init.cpp:30:
include/stan/math/prim/prob/std_normal_lccdf.hpp: In function 'stan::return_type_t<T> stan::math::std_normal_lccdf(const T_y&)':
include/stan/math/prim/prob/std_normal_lccdf.hpp:52: note: '-Wmisleading-indentation' is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers
52 | } else if (y_dbl > 8.25) {
include/stan/math/prim/prob/std_normal_lccdf.hpp:52: note: adding '-flarge-source-files' will allow for more column-tracking support, at the expense of compilation time and memory
gcc-14 -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 -DC99_INLINE_SEMANTICS=0 -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-14 -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 -DC99_INLINE_SEMANTICS=0 -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-14 -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 -DC99_INLINE_SEMANTICS=0 -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++-14 -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 -DC99_INLINE_SEMANTICS=0 -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 -DR_NO_REMAP -c stan_sampler.cpp -o stan_sampler.o
In file included from stan_sampler.hpp:4,
from stan_sampler.cpp:1:
include/ext/Rinternals.h:30:9: warning: "R_NO_REMAP" redefined
30 | #define R_NO_REMAP
| ^~~~~~~~~~
<command-line>: note: this is the location of the previous definition
In file included from include/stan/math/prim/prob/von_mises_lccdf.hpp:5,
from include/stan/math/prim/prob/von_mises_ccdf_log.hpp:4,
from include/stan/math/prim/prob.hpp:356,
from include/stan/math/prim.hpp:16,
from include/stan/io/dump.hpp:7,
from stan_sampler_includes.hpp:78,
from stan_sampler.hpp:15:
include/stan/math/prim/prob/von_mises_cdf.hpp: In function 'stan::return_type_t<T_x, T_sigma, T_l> stan::math::von_mises_cdf(const T_x&, const T_mu&, const T_k&)':
include/stan/math/prim/prob/von_mises_cdf.hpp:194: note: '-Wmisleading-indentation' is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers
194 | if (cdf_n < 0.0)
include/stan/math/prim/prob/von_mises_cdf.hpp:194: note: adding '-flarge-source-files' will allow for more column-tracking support, at the expense of compilation time and memory
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: At global scope:
include/stan/model/model_base_crtp.hpp:149: 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:3389: note: by 'continuous_model_namespace::continuous_model::log_prob'
3389 | inline T__ log_prob(std::vector<T__>& params_r,
include/stan/model/model_base_crtp.hpp:144: 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:3389: note: by 'continuous_model_namespace::continuous_model::log_prob'
3389 | inline T__ log_prob(std::vector<T__>& params_r,
include/stan/model/model_base_crtp.hpp:93: 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:3389: note: by 'continuous_model_namespace::continuous_model::log_prob'
3389 | inline T__ log_prob(std::vector<T__>& params_r,
include/stan/model/model_base_crtp.hpp:88: 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:3389: note: by 'continuous_model_namespace::continuous_model::log_prob'
3389 | inline T__ log_prob(std::vector<T__>& params_r,
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -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)