* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘RGBM’ ...
** package ‘RGBM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpASJKWE/R.INSTALL28a17440a2cff9/RGBM/src'
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c R_init_RGBM.c -o R_init_RGBM.o
gcc-14 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -c pcg_basic.c -o pcg_basic.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c solver_test.cpp -o solver_test.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c test_regression_stump.cpp -o test_regression_stump.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c test_regression_stump_R.cpp -o test_regression_stump_R.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c train_regression_stump.cpp -o train_regression_stump.o
train_regression_stump.cpp: In function ‘const Model train_regression_stump(int, int, const double*, const double*, double, double, int, int, double)’:
train_regression_stump.cpp:137:14: warning: unused variable ‘index_map’ [-Wunused-variable]
  137 |         int *index_map = (int*)calloc(N,sizeof(int));
      |              ^~~~~~~~~
train_regression_stump.cpp:170:16: warning: variable ‘best_rho_l’ set but not used [-Wunused-but-set-variable]
  170 |         double best_rho_l;
      |                ^~~~~~~~~~
train_regression_stump.cpp:171:16: warning: variable ‘best_rho_r’ set but not used [-Wunused-but-set-variable]
  171 |         double best_rho_r;
      |                ^~~~~~~~~~
train_regression_stump.cpp:174:9: warning: unused variable ‘k_t’ [-Wunused-variable]
  174 |   int t,k_t;
      |         ^~~
train_regression_stump.cpp:490:28: warning: ‘best_gamma_l’ may be used uninitialized [-Wmaybe-uninitialized]
  490 |               F[row] += nu * best_gamma_l;
      |                         ~~~^~~~~~~~~~~~~~
train_regression_stump.cpp:168:16: note: ‘best_gamma_l’ was declared here
  168 |         double best_gamma_l;
      |                ^~~~~~~~~~~~
train_regression_stump.cpp:492:28: warning: ‘best_gamma_r’ may be used uninitialized [-Wmaybe-uninitialized]
  492 |               F[row] += nu * best_gamma_r;
      |                         ~~~^~~~~~~~~~~~~~
train_regression_stump.cpp:169:16: note: ‘best_gamma_r’ was declared here
  169 |         double best_gamma_r;
      |                ^~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c train_regression_stump_R.cpp -o train_regression_stump_R.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o RGBM.so R_init_RGBM.o pcg_basic.o solver_test.o test_regression_stump.o test_regression_stump_R.o train_regression_stump.o train_regression_stump_R.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpASJKWE/R.INSTALL28a17440a2cff9/RGBM/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpASJKWE/R.INSTALL28a17440a2cff9/RGBM/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpASJKWE/R.INSTALL28a17440a2cff9/RGBM/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-RGBM/00new/RGBM/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘RGBM’
    finding HTML links ... done
    GBM                                     html  
    GBM.test                                html  
    GBM.train                               html  
    RGBM                                    html  
    RGBM.test                               html  
    RGBM.train                              html  
    add_names                               html  
    apply_row_deviation                     html  
    consider_previous_information           html  
    first_GBM_step                          html  
    get_colids                              html  
    get_filepaths                           html  
    get_ko_experiments                      html  
    get_tf_indices                          html  
    normalize_matrix_colwise                html  
    null_model_refinement_step              html  
    regularized_GBM_step                    html  
    regulate_regulon_size                   html  
    second_GBM_step                         html  
    select_ideal_k                          html  
    test_regression_stump_R                 html  
    train_regression_stump_R                html  
    transform_importance_to_weights         html  
    v2l                                     html  
    z_score_effect                          html  
** 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 (RGBM)