Install log for 'stan4bart'

* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* 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++-13 -std=gnu++17 accepts -g... yes
checking for g++-13 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++-13 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++-13 -std=gnu++17 accepts -g... (cached) yes
checking for g++-13 -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-13
checking whether the compiler supports GNU C... yes
checking whether gcc-13 accepts -g... yes
checking for gcc-13 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... 14:756e6547:6c65746e:49656e69
checking for x86 cpuid 0x00000001 output... 406f1:200800:7ffefbff: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-13 (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpy0bK4K/R.INSTALL1807275d3d8cb8/stan4bart/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/dbarts/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bart_util.cpp -o bart_util.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/dbarts/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c init.cpp -o init.o
In file included from include/stan/math/rev/fun.hpp:128,
                 from include/stan/math/rev.hpp:10,
                 from include/stan/model/gradient.hpp:6,
                 from include/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp:6,
                 from include/stan/mcmc/hmc/hamiltonians/diag_e_metric.hpp:5,
                 from include/stan/mcmc/hmc/nuts/diag_e_nuts.hpp:6,
                 from include/stan/mcmc/hmc/nuts/adapt_diag_e_nuts.hpp:6,
                 from interruptable_sampler.hpp:68,
                 from stan_sampler.hpp:18,
                 from init.cpp:30:
include/stan/math/rev/fun/matrix_power.hpp: In function ‘stan::plain_type_t<T> stan::math::matrix_power(const T&, int)’:
include/stan/math/rev/fun/matrix_power.hpp:33: note: ‘-Wmisleading-indentation’ is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers
   33 |   if (M.size() == 0)
      | 
include/stan/math/rev/fun/matrix_power.hpp:33: note: adding ‘-flarge-source-files’ will allow for more column-tracking support, at the expense of compilation time and memory
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/dbarts/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c misc_adaptiveRadixTree.c -o misc_adaptiveRadixTree.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/dbarts/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c misc_string.c -o misc_string.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/dbarts/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c rc_bounds.c -o rc_bounds.o
gcc-13 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/dbarts/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c rc_util.c -o rc_util.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG -I"include" -I"include/sundials" -I"../inst/include" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/BH/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppEigen/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/dbarts/include' -I/usr/local/include -D_FORTIFY_SOURCE=3  -I'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c stan_sampler.cpp -o stan_sampler.o
In file included from include/stan/math/rev/fun.hpp:128,
                 from include/stan/math/rev.hpp:10,
                 from include/stan/model/gradient.hpp:6,
                 from include/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp:6,
                 from include/stan/mcmc/hmc/hamiltonians/diag_e_metric.hpp:5,
                 from include/stan/mcmc/hmc/nuts/diag_e_nuts.hpp:6,
                 from include/stan/mcmc/hmc/nuts/adapt_diag_e_nuts.hpp:6,
                 from interruptable_sampler.hpp:68,
                 from stan_sampler.hpp:18,
                 from stan_sampler.cpp:1:
include/stan/math/rev/fun/matrix_power.hpp: In function ‘stan::plain_type_t<T> stan::math::matrix_power(const T&, int)’:
include/stan/math/rev/fun/matrix_power.hpp:33: note: ‘-Wmisleading-indentation’ is disabled from this point onwards, since column-tracking was disabled due to the size of the code/headers
   33 |   if (M.size() == 0)
      | 
include/stan/math/rev/fun/matrix_power.hpp:33: 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++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -Wl,-O1 -o stan4bart.so bart_util.o init.o misc_adaptiveRadixTree.o misc_string.o rc_bounds.o rc_util.o stan_sampler.o -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/lib/ -Wl,-rpath,/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/lib/ -ltbb -ltbbmalloc -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpy0bK4K/R.INSTALL1807275d3d8cb8/stan4bart/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpy0bK4K/R.INSTALL1807275d3d8cb8/stan4bart/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpy0bK4K/R.INSTALL1807275d3d8cb8/stan4bart/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/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)