* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘shaman’ ...
** this is package ‘shaman’ version ‘2.1.1’
** package ‘shaman’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
specified C++17
using C++ compiler: ‘g++-16 (Debian 16.2.0-3) 16.2.0’
using C++17
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcHnu5I/R.INSTALL271f596cb1e6dc/shaman/src'
g++-16 -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/usr/local/include -D_FORTIFY_SOURCE=3  -pthread -fpic  -g -O2 -Wall -pedantic -mtune=native   -c ContactShuffler.cpp -o ContactShuffler.o
g++-16 -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/usr/local/include -D_FORTIFY_SOURCE=3  -pthread -fpic  -g -O2 -Wall -pedantic -mtune=native   -c GenomeGridLog.cpp -o GenomeGridLog.o
g++-16 -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/usr/local/include -D_FORTIFY_SOURCE=3  -pthread -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Parser.cpp -o Parser.o
g++-16 -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/usr/local/include -D_FORTIFY_SOURCE=3  -pthread -fpic  -g -O2 -Wall -pedantic -mtune=native   -c Random.cpp -o Random.o
g++-16 -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/usr/local/include -D_FORTIFY_SOURCE=3  -pthread -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-16 -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/usr/local/include -D_FORTIFY_SOURCE=3  -pthread -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hic_matrix_shuffler.cpp -o hic_matrix_shuffler.o
g++-16 -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/usr/local/include -D_FORTIFY_SOURCE=3  -pthread -fpic  -g -O2 -Wall -pedantic -mtune=native   -c merge_ks.cpp -o merge_ks.o
g++-16 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o shaman.so ContactShuffler.o GenomeGridLog.o Parser.o Random.o RcppExports.o hic_matrix_shuffler.o merge_ks.o -pthread -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcHnu5I/R.INSTALL271f596cb1e6dc/shaman/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpcHnu5I/R.INSTALL271f596cb1e6dc/shaman/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpcHnu5I/R.INSTALL271f596cb1e6dc/shaman/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-shaman/00new/shaman/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 ‘shaman’
    finding HTML links ... done
    ctcf_forward                            html  
    ctcf_reverse                            html  
    dot-shaman_dump_config                  html  
    dot-shaman_load_config                  html  
    get_param                               html  
    get_param_list                          html  
    init_params                             html  
    shaman-package                          html  
    shaman_generate_feature_grid            html  
    shaman_get_test_track_db                html  
    shaman_gplot_map                        html  
    shaman_gplot_map_score                  html  
    shaman_kk_norm                          html  
    shaman_plot_feature_grid                html  
    shaman_plot_map_score_with_annotations
                                            html  
    shaman_plot_tracks_and_annotations      html  
    shaman_score_hic_mat                    html  
    shaman_score_hic_mat_for_track          html  
    shaman_score_hic_points                 html  
    shaman_score_hic_track                  html  
    shaman_score_pal                        html  
    shaman_shuffle_and_score_hic_mat        html  
    shaman_shuffle_hic_mat_for_track        html  
    shaman_shuffle_hic_track                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 (shaman)