* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pathfindR’ ...
** this is package ‘pathfindR’ version ‘3.0.1’
** package ‘pathfindR’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.3.0-1) 15.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJ6ZbXU/R.INSTALL2bbcc23ade7e9/pathfindR/src'
g++-15 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c greedy_search.cpp -o greedy_search.o
g++-15 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c java_compat.cpp -o java_compat.o
g++-15 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c pathfindR-package.cpp -o pathfindR-package.o
g++-15 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c score_calculation_utils.cpp -o score_calculation_utils.o
g++-15 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c simulated_annealing.cpp -o simulated_annealing.o
g++-15 -std=gnu++20 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c subnetwork_scoring.cpp -o subnetwork_scoring.o
g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o pathfindR.so RcppExports.o greedy_search.o java_compat.o pathfindR-package.o score_calculation_utils.o simulated_annealing.o subnetwork_scoring.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJ6ZbXU/R.INSTALL2bbcc23ade7e9/pathfindR/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpJ6ZbXU/R.INSTALL2bbcc23ade7e9/pathfindR/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpJ6ZbXU/R.INSTALL2bbcc23ade7e9/pathfindR/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-pathfindR/00new/pathfindR/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 ‘pathfindR’
finding HTML links ... done
UpSet_plot html
active_snw_enrichment_wrapper html
active_subnetwork_search html
annotate_term_genes html
build_network html
build_score_context html
cluster_enriched_terms html
cluster_graph_vis html
color_kegg_pathway html
combine_pathfindR_results html
combined_results_graph html
create_HTML_report html
create_kappa_matrix html
create_term_gene_graph html
create_term_gene_plot html
dot-find_components_named html
dot-find_subnetworks html
dot-ga_compare html
dot-ga_crossover_mutation html
dot-ga_make_individual html
dot-ga_pick html
dot-ga_score html
dot-ga_sort_desc html
dot-genetic_algorithm html
dot-greedy_search html
dot-make_subnetwork html
dot-parse_experiment html
dot-score_subnetwork html
dot-simulated_annealing html
dot-sort_subnetworks_desc html
enrichment html
enrichment_analyses html
enrichment_chart html
example_unfiltered_snws html
fetch_gene_sets html
filter_active_subnetworks html
fuzzy_term_clustering html
get_active_subnetworks html
get_biogrid_pin html
get_gene_sets_list html
get_kegg_gsets html
get_mgsigdb_gsets html
get_pin_file html
get_reactome_gsets html
gset_list_from_gmt html
hierarchical_term_clustering html
hyperg_test html
input_processing html
input_testing html
isColor html
order_df_by_columnn html
pathfindR html
plot_scores html
process_pin html
return_pin_path html
run_pathfindR html
safe_get_content html
score_terms html
single_iter_wrapper html
summarize_enrichment_results html
term_gene_heatmap html
visualize_KEGG_diagram html
visualize_active_subnetworks html
visualize_term_interactions html
visualize_terms 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 (pathfindR)