* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘pathfindR’ ... ** this is package ‘pathfindR’ version ‘3.0.2’ ** package ‘pathfindR’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmSZsRA/R.INSTALL49fab3cda694d/pathfindR/src' g++-16 -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++-16 -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++-16 -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++-16 -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++-16 -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++-16 -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++-16 -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++-16 -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/RtmpmSZsRA/R.INSTALL49fab3cda694d/pathfindR/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpmSZsRA/R.INSTALL49fab3cda694d/pathfindR/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpmSZsRA/R.INSTALL49fab3cda694d/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)