* installing *source* package ‘VCBART’ ...
** this is package ‘VCBART’ version ‘1.2.4’
** package ‘VCBART’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/VCBART/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 funs.cpp -o funs.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 predict_vcbart.cpp -o predict_vcbart.o
In file included from rng.h:3,
from tree.h:5,
from funs.h:6,
from funs.cpp:1:
helpers.h: In member function ‘std::set<int> set_str_conversion::hex_to_set(int&, std::string&)’:
helpers.h:260:23: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
260 | if(hex_str.size() != num_blocks+1){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
funs.cpp: In function ‘void fit_ensemble(std::vector<double>&, std::vector<tree>&, data_info&)’:
funs.cpp:46:17: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
46 | if(fit.size() != di.N) Rcpp::stop("[fit_ensemble]: size of fit must be equal to di.N!"); // honestly should never get triggered
| ~~~~~~~~~~~^~~~~~~
funs.cpp:53:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<tree>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
53 | for(int m = 0; m < t_vec.size(); m++) fit[i] += t_vec[m].evaluate(zz_cont, zz_cat); // involves a tree traversal
| ~~^~~~~~~~~~~~~~
funs.cpp: In function ‘void graph_partition(std::set<int>&, std::set<int>&, std::set<int>&, std::vector<edge>&, int&, int&, RNG&)’:
funs.cpp:1060:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<int, std::allocator<int> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1060 | for(int comp_ix = 0; comp_ix < components.size(); comp_ix++){
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~
funs.cpp:1096:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<edge>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
1096 | for(int e = 0; e < mst_edges.size(); e++){
| ~~^~~~~~~~~~~~~~~~~~
In file included from rng.h:3,
from tree.h:5,
from funs.h:6,
from predict_vcbart.cpp:1:
helpers.h: In member function ‘std::set<int> set_str_conversion::hex_to_set(int&, std::string&)’:
helpers.h:260:23: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
260 | if(hex_str.size() != num_blocks+1){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
funs.cpp: In function ‘void update_theta_u(std::vector<double>&, double&, std::vector<int, std::allocator<int> >&, int&, double&, double&, RNG&)’:
funs.cpp:1122:19: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
1122 | if(theta.size() != R){
| ~~~~~~~~~~~~~^~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 rescale_beta.cpp -o rescale_beta.o
funs.cpp: In function ‘void compute_suff_stat_grow(suff_stat&, suff_stat&, int&, rule_t&, tree&, data_info&)’:
funs.cpp:130:131: warning: ‘zz_cont’ may be used uninitialized [-Wmaybe-uninitialized]
130 | for(rc_it rcit = rule.rc_weight.begin(); rcit != rule.rc_weight.end(); ++rcit) tmp_z += (rcit->second) * zz_cont[rcit->first];
| ^
funs.cpp:59:11: note: ‘zz_cont’ was declared here
59 | double* zz_cont;
| ^~~~~~~
funs.cpp:109:52: warning: ‘zz_cat’ may be used uninitialized [-Wmaybe-uninitialized]
109 | l_count = rule.l_vals.count(zz_cat[rule.v_cat]);
| ^
funs.cpp:60:8: note: ‘zz_cat’ was declared here
60 | int* zz_cat;
| ^~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 rng.cpp -o rng.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 tree.cpp -o tree.o
In file included from rng.h:3,
from rng.cpp:1:
helpers.h: In member function ‘std::set<int> set_str_conversion::hex_to_set(int&, std::string&)’:
helpers.h:260:23: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
260 | if(hex_str.size() != num_blocks+1){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
rng.cpp: In member function ‘arma::vec RNG::mvnormal(arma::vec, arma::mat)’:
rng.cpp:107:17: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
107 | if( (P.n_rows != d) | (P.n_cols != d)){
| ~~~~~~~~~^~~~
rng.cpp:107:35: warning: comparison of integer expressions of different signedness: ‘const arma::uword’ {aka ‘const unsigned int’} and ‘int’ [-Wsign-compare]
107 | if( (P.n_rows != d) | (P.n_cols != d)){
| ~~~~~~~~~^~~~
In file included from rng.h:3,
from tree.h:5,
from tree.cpp:4:
helpers.h: In member function ‘std::set<int> set_str_conversion::hex_to_set(int&, std::string&)’:
helpers.h:260:23: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
260 | if(hex_str.size() != num_blocks+1){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 update_trees.cpp -o update_trees.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 vcbart_cs_fit.cpp -o vcbart_cs_fit.o
In file included from rng.h:3,
from tree.h:5,
from funs.h:6,
from update_trees.h:4,
from vcbart_cs_fit.cpp:1:
helpers.h: In member function ‘std::set<int> set_str_conversion::hex_to_set(int&, std::string&)’:
helpers.h:260:23: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
260 | if(hex_str.size() != num_blocks+1){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
In file included from rng.h:3,
from tree.h:5,
from funs.h:6,
from update_trees.h:4,
from update_trees.cpp:1:
helpers.h: In member function ‘std::set<int> set_str_conversion::hex_to_set(int&, std::string&)’:
helpers.h:260:23: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
260 | if(hex_str.size() != num_blocks+1){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/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 vcbart_ind_fit.cpp -o vcbart_ind_fit.o
In file included from /usr/include/c++/15/x86_64-redhat-linux/bits/c++allocator.h:33,
from /usr/include/c++/15/bits/allocator.h:46,
from /usr/include/c++/15/bits/alloc_traits.h:39,
from /usr/include/c++/15/ext/alloc_traits.h:36,
from /usr/include/c++/15/bits/hashtable_policy.h:39,
from /usr/include/c++/15/bits/hashtable.h:37,
from /usr/include/c++/15/bits/unordered_map.h:33,
from /usr/include/c++/15/unordered_map:43,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/platform/compiler.h:39,
from /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/r/headers.h:67,
from /data/gannet/ripley/R/test-dev/Rcpp/include/RcppCommon.h:31,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
from /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo.h:32,
from helpers.h:4:
In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = tree]’,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::deallocate(allocator_type&, pointer, size_type) [with _Tp = tree]’ at /usr/include/c++/15/bits/alloc_traits.h:649:23,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = tree; _Alloc = std::allocator<tree>]’ at /usr/include/c++/15/bits/stl_vector.h:396:19,
inlined from ‘void std::_Vector_base<_Tp, _Alloc>::_M_deallocate(pointer, std::size_t) [with _Tp = tree; _Alloc = std::allocator<tree>]’ at /usr/include/c++/15/bits/stl_vector.h:392:7,
inlined from ‘std::_Vector_base<_Tp, _Alloc>::~_Vector_base() [with _Tp = tree; _Alloc = std::allocator<tree>]’ at /usr/include/c++/15/bits/stl_vector.h:375:15,
inlined from ‘std::vector<_Tp, _Alloc>::~vector() [with _Tp = tree; _Alloc = std::allocator<tree>]’ at /usr/include/c++/15/bits/stl_vector.h:805:7,
inlined from ‘Rcpp::List vcbart_cs_fit(Rcpp::NumericVector, double, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::IntegerMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::IntegerMatrix, Rcpp::LogicalVector, Rcpp::Nullable<Rcpp::Vector<19> >, Rcpp::Nullable<Rcpp::Vector<19> >, Rcpp::Nullable<Rcpp::Vector<19> >, Rcpp::LogicalVector, int, bool, double, double, double, bool, double, double, Rcpp::NumericVector, Rcpp::NumericVector, double, double, int, int, int, int, bool, bool, bool, int)’ at vcbart_cs_fit.cpp:202:51:
/usr/include/c++/15/bits/new_allocator.h:172:66: warning: ‘void operator delete(void*, std::size_t)’ called on pointer ‘__first’ with nonzero offset 200 [-Wfree-nonheap-object]
172 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n));
| ^
vcbart_cs_fit.cpp: In function ‘Rcpp::List vcbart_cs_fit(Rcpp::NumericVector, double, Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::IntegerMatrix, Rcpp::NumericMatrix, Rcpp::NumericMatrix, Rcpp::IntegerMatrix, Rcpp::LogicalVector, Rcpp::Nullable<Rcpp::Vector<19> >, Rcpp::Nullable<Rcpp::Vector<19> >, Rcpp::Nullable<Rcpp::Vector<19> >, Rcpp::LogicalVector, int, bool, double, double, double, bool, double, double, Rcpp::NumericVector, Rcpp::NumericVector, double, double, int, int, int, int, bool, bool, bool, int)’:
vcbart_cs_fit.cpp:4:12: note: declared here
4 | Rcpp::List vcbart_cs_fit(Rcpp::NumericVector Y_train,
| ^~~~~~~~~~~~~
In file included from rng.h:3,
from tree.h:5,
from funs.h:6,
from update_trees.h:4,
from vcbart_ind_fit.cpp:1:
helpers.h: In member function ‘std::set<int> set_str_conversion::hex_to_set(int&, std::string&)’:
helpers.h:260:23: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
260 | if(hex_str.size() != num_blocks+1){
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o VCBART.so RcppExports.o funs.o predict_vcbart.o rescale_beta.o rng.o tree.o update_trees.o vcbart_cs_fit.o vcbart_ind_fit.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/VCBART/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/VCBART/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/VCBART/src'
installing to /data/gannet/ripley/R/packages/tests-devel/VCBART.Rcheck/00LOCK-VCBART/00new/VCBART/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 (VCBART)