* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘numbat’ ... ** package ‘numbat’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-6) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9HyD5v/R.INSTALL2ebe6093a8ed8/numbat/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I"../inst/include" -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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/roptim/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -I"../inst/include" -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.cpp -o misc.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o numbat.so RcppExports.o misc.o -lpthread -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9HyD5v/R.INSTALL2ebe6093a8ed8/numbat/src' make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9HyD5v/R.INSTALL2ebe6093a8ed8/numbat/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9HyD5v/R.INSTALL2ebe6093a8ed8/numbat/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-numbat/00new/numbat/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 ‘numbat’ finding HTML links ... done Modes html Numbat html acen_hg19 html acen_hg38 html aggregate_counts html analyze_bulk html annot_consensus html annot_haplo_segs html annot_ref html annot_segs html annot_theta_mle html annot_theta_roll html annotate_genes html approx_phi_post html approx_theta_post html binary_entropy html bulk_example html calc_allele_LLR html calc_allele_lik html calc_cluster_dist html calc_exp_LLR html calc_phi_mle_lnpois html check_allele_df html check_contam html check_exp_noise html check_exp_ref html check_matrix html check_segs_fix html check_segs_loh html choose_ref_cor html chrom_sizes_hg19 html chrom_sizes_hg38 html classify_alleles html cnv_heatmap html combine_bulk html compute_posterior html contract_nodes html count_mat_example html count_mat_ref html detect_clonal_loh html df_allele_example html exp_hclust html expand_states html fill_neu_segs html filter_genes html find_common_diploid html fit_bbinom html fit_gamma html fit_lnpois html fit_ref_sse html fit_snp_rate html gaps_hg19 html gaps_hg38 html generate_postfix html genotype html get_allele_bulk html get_allele_hmm html get_allele_post html get_bulk html get_clone_post html get_exp_bulk html get_exp_likelihoods html get_exp_post html get_exp_sc html get_gtree html get_haplotype_post html get_inter_cm html get_internal_nodes html get_joint_post html get_lambdas_bar html get_move_cost html get_move_opt html get_nodes_celltree html get_ordered_tips html get_segs_consensus html get_segs_neu html get_snps html get_tree_post html gexp_roll_example html gtf_hg19 html gtf_hg38 html gtf_mm10 html hc_example html joint_post_example html label_edges html label_genotype html log_mem html log_message html make_group_bulks html mark_tumor_lineage html mut_graph_example html phi_hat_roll html phi_hat_seg html phylogeny_example html plot_bulks html plot_consensus html plot_exp_roll html plot_mut_history html plot_phylo_heatmap html plot_psbulk html plot_sc_tree html pnorm.range.log html pre_likelihood_hmm html preprocess_allele html ref_hca html ref_hca_counts html relevel_chrom html resolve_cnvs html retest_bulks html retest_cnv html return_missing_columns html run_group_hmms html run_numbat html segs_example html simes_p html simplify_history html smooth_expression html smooth_segs html switch_prob_cm html t_test_pval html test_multi_allelic html theta_hat_roll html theta_hat_seg html transfer_links html upgma html vcf_meta html viterbi_loh 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 (numbat)