* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘bcf’ ...
** package ‘bcf’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFX2OMN/R.INSTALL36b7ec43ec4245/bcf/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c TreeSamples.cpp -o TreeSamples.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c bcf_clean.cpp -o bcf_clean.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c bcf_clean_overpar.cpp -o bcf_clean_overpar.o
bcf_clean_overpar.cpp:106:3: warning: "/*" within comment [-Wcomment]
106 | /* Read, format y
bcf_clean_overpar.cpp:126:3: warning: "/*" within comment [-Wcomment]
126 | /* Read, format weights
bcf_clean_overpar.cpp:137:3: warning: "/*" within comment [-Wcomment]
137 | /* Read, format X_con
bcf_clean_overpar.cpp:162:3: warning: "/*" within comment [-Wcomment]
162 | /* Read, format X_mod
bcf_clean_overpar.cpp:193:3: warning: "/*" within comment [-Wcomment]
193 | /* Setup the model
bcf_clean_overpar.cpp: In function ‘Rcpp::List bcfoverparRcppClean(Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::List, Rcpp::List, arma::mat, arma::mat, arma::mat, double, int, int, int, int, int, double, double, double, double, double, double, double, double, Rcpp::CharacterVector, Rcpp::CharacterVector, int, bool, bool, bool, bool, double, bool, bool)’:
bcf_clean_overpar.cpp:131:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
131 | for(int j=0; j<n; j++) {
| ~^~
bcf_clean_overpar.cpp:152:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
152 | for(int i=0; i<p_con; ++i) {
| ~^~~~~~
bcf_clean_overpar.cpp:155:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
155 | for(size_t j=0; j<tmp.size(); ++j) {
| ~^~~~~~~~~~~
bcf_clean_overpar.cpp:180:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
180 | for(int i=0; i<p_mod; ++i) {
| ~^~~~~~
bcf_clean_overpar.cpp:183:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
183 | for(size_t j=0; j<tmp.size(); ++j) {
| ~^~~~~~~~~~~
bcf_clean_overpar.cpp:198:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
198 | for(size_t i=0;i<ntree_mod;i++) t_mod[i].setm(trt_init/(double)ntree_mod);
| ~^~~~~~~~~~
bcf_clean_overpar.cpp:201:19: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
201 | for(size_t i=0;i<ntree_con;i++) t_con[i].setm(ybar/(double)ntree_con);
| ~^~~~~~~~~~
bcf_clean_overpar.cpp:277:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
277 | for(size_t k=0; k<nr; ++k) {
| ~^~~
bcf_clean_overpar.cpp:346:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
346 | for(size_t iIter=0;iIter<(nd*thin+burn);iIter++) {
| ~~~~~^~~~~~~~~~~~~~~
bcf_clean_overpar.cpp:378:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
378 | for (int k=0; k<n; ++k){
| ~^~
bcf_clean_overpar.cpp:382:22: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
382 | for(size_t k=0; k<ntrt; ++k) {
| ~^~~~~
bcf_clean_overpar.cpp:394:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
394 | for(size_t iTreeCon=0;iTreeCon<ntree_con;iTreeCon++) {
| ~~~~~~~~^~~~~~~~~~
bcf_clean_overpar.cpp:525:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
525 | for(size_t iTreeMod=0;iTreeMod<ntree_mod;iTreeMod++) {
| ~~~~~~~~^~~~~~~~~~
bcf_clean_overpar.cpp:556:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
556 | double bscale = (k<ntrt) ? bscale1 : bscale0;
| ~^~~~~
bcf_clean_overpar.cpp:623:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
623 | for(size_t k=0;k<ntrt;k++) {
| ~^~~~~
bcf_clean_overpar.cpp:653:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
653 | double bscale = (k<ntrt) ? bscale1 : bscale0;
| ~^~~~~
bcf_clean_overpar.cpp:669:13: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
669 | if(k<ntrt) {
| ~^~~~~
bcf_clean_overpar.cpp:703:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
703 | for(size_t k=0; k<ntrt; ++k) {
| ~^~~~~
bcf_clean_overpar.cpp:716:39: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
716 | for(size_t iTreeMod=0;iTreeMod<ntree_mod;iTreeMod++) {
| ~~~~~~~~^~~~~~~~~~
bcf_clean_overpar.cpp:793:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
793 | for(size_t iTreeCon=0;iTreeCon<ntree_con;iTreeCon++) {
| ~~~~~~~~^~~~~~~~~~
bcf_clean_overpar.cpp:898:16: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
898 | if( ((iIter>=burn) & (iIter % thin==0)) ) {
| ~~~~~^~~~~~
bcf_clean_overpar.cpp:900:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
900 | for(size_t j=0;j<ntree_con;j++) treef_con << std::setprecision(save_tree_precision) << t_con[j] << endl; // save trees
| ~^~~~~~~~~~
bcf_clean_overpar.cpp:901:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
901 | for(size_t j=0;j<ntree_mod;j++) treef_mod << std::setprecision(save_tree_precision) << t_mod[j] << endl; // save trees
| ~^~~~~~~~~~
bcf_clean_overpar.cpp:919:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
919 | double bscale = (k<ntrt) ? bscale1 : bscale0;
| ~^~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c bd.cpp -o bd.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c funs.cpp -o funs.o
funs.cpp: In function ‘void allsuff(tree&, xinfo&, dinfo&, double*, tree::npv&, std::vector<sinfo>&)’:
funs.cpp:279:23: warning: unused variable ‘tbn’ [-Wunused-variable]
279 | tree::tree_cp tbn; //the pointer to the bottom node for the current observations
| ^~~
funs.cpp:280:16: warning: unused variable ‘ni’ [-Wunused-variable]
280 | size_t ni; //the index into vector of the current bottom node
| ^~
funs.cpp:281:17: warning: unused variable ‘xx’ [-Wunused-variable]
281 | double *xx; //current x
| ^~
funs.cpp:282:16: warning: unused variable ‘y’ [-Wunused-variable]
282 | double y; //current y
| ^
funs.cpp: In function ‘std::vector<int, std::allocator<int> > counts(tree&, xinfo&, dinfo&, tree::npv&)’:
funs.cpp:318:16: warning: variable ‘y’ set but not used [-Wunused-but-set-variable]
318 | double y; //current y
| ^
funs.cpp:324:14: warning: unused variable ‘nb’ [-Wunused-variable]
324 | bvsz nb = bnv.size();
| ^~
funs.cpp: In function ‘void update_counts(int, std::vector<int, std::allocator<int> >&, tree&, xinfo&, dinfo&, tree::npv&, int)’:
funs.cpp:351:16: warning: variable ‘y’ set but not used [-Wunused-but-set-variable]
351 | double y; //current y
| ^
funs.cpp:354:14: warning: unused variable ‘nb’ [-Wunused-variable]
354 | bvsz nb = bnv.size();
| ^~
funs.cpp: In function ‘void update_counts(int, std::vector<int, std::allocator<int> >&, tree&, xinfo&, dinfo&, std::map<const tree*, long unsigned int>&, int)’:
funs.cpp:376:16: warning: variable ‘y’ set but not used [-Wunused-but-set-variable]
376 | double y; //current y
| ^
funs.cpp: In function ‘void update_counts(int, std::vector<int, std::allocator<int> >&, tree&, xinfo&, dinfo&, std::map<const tree*, long unsigned int>&, int, const tree*&)’:
funs.cpp:404:10: warning: variable ‘y’ set but not used [-Wunused-but-set-variable]
404 | double y; //current y
| ^
funs.cpp: In function ‘void drmu(tree&, xinfo&, dinfo&, pinfo&, double*, RNG&)’:
funs.cpp:1123:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
1123 | for(int j=0; j<di.n; ++j) Rcout << *(di.x + j*di.p) <<" "; //*(x + p*i+j)
| ~^~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24,
from funs.cpp:4:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here
251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id);
| ~~~~~~~~~^~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here
291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL )
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TinyThread.h:7,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:6:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/Common.h: In instantiation of ‘int RcppParallel::resolveValue(const char*, T, U) [with T = long unsigned int; U = int]’:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:60:28: required from ‘void RcppParallel::parallelReduce(std::size_t, std::size_t, Reducer&, std::size_t, int) [with Reducer = AllSuffWorker; std::size_t = long unsigned int]’
60 | grainSize = resolveValue("RCPP_PARALLEL_GRAIN_SIZE", grainSize, 1);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
funs.cpp:303:16: required from here
303 | parallelReduce(0, di.n, asw);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/Common.h:16:23: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
16 | if (requestedValue != defaultValue && requestedValue > 0)
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c logging.cpp -o logging.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c rng.cpp -o rng.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -DRCPP_PARALLEL_USE_TBB=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c tree.cpp -o tree.o
tree.cpp: In member function ‘void tree::pr(xinfo&) const’:
tree.cpp:596:16: warning: variable ‘pid’ set but not used [-Wunused-but-set-variable]
596 | size_t pid;
| ^~~
tree.cpp: In member function ‘void tree::pr() const’:
tree.cpp:636:16: warning: variable ‘pid’ set but not used [-Wunused-but-set-variable]
636 | size_t pid;
| ^~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o bcf.so RcppExports.o TreeSamples.o bcf_clean.o bcf_clean_overpar.o bd.o funs.o logging.o rng.o tree.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFX2OMN/R.INSTALL36b7ec43ec4245/bcf/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFX2OMN/R.INSTALL36b7ec43ec4245/bcf/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFX2OMN/R.INSTALL36b7ec43ec4245/bcf/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bcf/00new/bcf/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘bcf’
finding HTML links ... done
bcf html
predict.bcf html
summary.bcf html
** 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 (bcf)