* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘sigminer’ ... ** package ‘sigminer’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpetpOH8/R.INSTALL3e7acb449ae201/sigminer/src' g++-14 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-14 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c calc_cosine.cpp -o calc_cosine.o g++-14 -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 -fpic -g -O2 -Wall -pedantic -mtune=native -c get_intersect_size.cpp -o get_intersect_size.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o sigminer.so RcppExports.o calc_cosine.o get_intersect_size.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpetpOH8/R.INSTALL3e7acb449ae201/sigminer/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpetpOH8/R.INSTALL3e7acb449ae201/sigminer/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpetpOH8/R.INSTALL3e7acb449ae201/sigminer/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-sigminer/00new/sigminer/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to 'sqrt' ** help *** installing help indices converting help for package ‘sigminer’ finding HTML links ... done CN.features html CopyNumber-class html MAF-class html add_h_arrow html add_labels html bp html centromeres.T2T html centromeres.hg19 html centromeres.hg38 html centromeres.mm10 html centromeres.mm9 html chromsize.T2T html chromsize.hg19 html chromsize.hg38 html chromsize.mm10 html chromsize.mm9 html cosine html cytobands.T2T html cytobands.hg19 html cytobands.hg38 html cytobands.mm10 html cytobands.mm9 html enrich_component_strand_bias html get_Aneuploidy_score html get_adj_p html get_bayesian_result html get_cn_freq_table html get_cn_ploidy html get_genome_annotation html get_group_comparison html get_groups html get_intersect_size html get_pLOH_score html get_shannon_diversity_index html get_sig_cancer_type_index html get_sig_db html get_sig_exposure html get_sig_feature_association html get_sig_rec_similarity html get_sig_similarity html get_tidy_association html group_enrichment html group_enrichment2 html handle_hyper_mutation html hello html output_bootstrap html output_fit html output_sig html output_tally html pipe html read_copynumber html read_copynumber_ascat html read_copynumber_seqz html read_maf html read_sv_as_rs html read_vcf html read_xena_variants html report_bootstrap_p_value html same_size_clustering html scoring html show_catalogue html show_cn_circos html show_cn_components html show_cn_distribution html show_cn_features html show_cn_freq_circos html show_cn_group_profile html show_cn_profile html show_cor html show_cosmic html show_cosmic_sig_profile html show_group_comparison html show_group_distribution html show_group_enrichment html show_group_mapping html show_groups html show_sig_bootstrap html show_sig_consensusmap html show_sig_exposure html show_sig_feature_corrplot html show_sig_fit html show_sig_profile html show_sig_profile_heatmap html show_sig_profile_loop html sig_auto_extract html sig_convert html sig_estimate html sig_extract html sig_fit html sig_fit_bootstrap html sig_fit_bootstrap_batch html sig_operation html sig_tally html sig_unify_extract html sigminer-package html sigprofiler html simulated_catalogs html simulation html subset.CopyNumber html tidyeval html transcript.T2T html transcript.hg19 html transcript.hg38 html transcript.mm10 html transcript.mm9 html transform_seg_table html use_color_style 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 (sigminer)