* installing to library ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages’
* installing *source* package ‘bcf’ ...
** package ‘bcf’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcknSKh/R.INSTALL271d1b74569abf/bcf/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TinyThread.h:7,
                 from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:6,
                 from funs.cpp:4:
/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:57:28:   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]’
funs.cpp:303:16:   required from here
/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-gcc/Work/build/include" -DNDEBUG  -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/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-devel-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++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-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-devel-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcknSKh/R.INSTALL271d1b74569abf/bcf/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcknSKh/R.INSTALL271d1b74569abf/bcf/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcknSKh/R.INSTALL271d1b74569abf/bcf/src'
installing to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/00LOCK-bcf/00new/bcf/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* creating tarball
packaged installation of ‘bcf’ as ‘bcf_2.0.2_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (bcf)