* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘bonsaiforest’ ...
** package ‘bonsaiforest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.3.0-1) 13.3.0’
make[1]: Entering directory '/tmp/RtmprQ9pv3/R.INSTALL34a3ca1afeb704/bonsaiforest/src'
g++-13 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -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-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/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c surv_prob.cpp -o surv_prob.o
surv_prob.cpp: In function ‘Rcpp::List surv_prob(arma::mat, arma::mat)’:
surv_prob.cpp:7:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
7 | for (int i = 0; i < h.n_cols; i++){
| ~~^~~~~~~~~~
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o bonsaiforest.so RcppExports.o surv_prob.o -fopenmp -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 '/tmp/RtmprQ9pv3/R.INSTALL34a3ca1afeb704/bonsaiforest/src'
make[1]: Entering directory '/tmp/RtmprQ9pv3/R.INSTALL34a3ca1afeb704/bonsaiforest/src'
make[1]: Leaving directory '/tmp/RtmprQ9pv3/R.INSTALL34a3ca1afeb704/bonsaiforest/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-bonsaiforest/00new/bonsaiforest/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘bonsaiforest’
finding HTML links ... done
ahr_estimation html
ahr_from_km html
bonsaiforest-package html
compare html
cut_norm_quant html
design_dummy1 html
design_matrix1 html
elastic_net html
elastic_net_fit_bin html
elastic_net_fit_surv html
elastic_net_surv html
est_coef_bin1 html
example_data html
generate_stacked_data html
horseshoe html
horseshoe_fit_bin html
horseshoe_fit_surv html
km_fun html
lor_estimation html
naive html
naive_fit_bin html
naive_fit_surv html
naivepop html
naivepop_fit_bin html
naivepop_fit_surv html
plot.compare.data html
plot.summary.elastic_net html
plot.summary.horseshoe html
plot.summary.naive html
preprocess html
print.summary.elastic_net html
print.summary.horseshoe html
print.summary.naive html
print.summary.naivepop html
simul_covariates html
simul_data html
simul_pfs html
subgroups html
summary.elastic_net html
summary.horseshoe html
summary.naive html
summary.naivepop html
survival_curves html
trt_horseshoe html
*** copying figures
** 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 (bonsaiforest)