* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘mappoly’ ... ** package ‘mappoly’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-1) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpG6Z4KT/R.INSTALL1f27c95486d764/mappoly/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/RcppParallel/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'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calc_genoprob.cpp -o calc_genoprob.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calc_genoprob_based_on_phased_marker_blocks.cpp -o calc_genoprob_based_on_phased_marker_blocks.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calc_loglike_given_map.cpp -o calc_loglike_given_map.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c combinatorial.cpp -o combinatorial.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c est_hmm_map_based_on_phased_mrk_blocks.cpp -o est_hmm_map_based_on_phased_mrk_blocks.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c est_map_hmm_given_dose.cpp -o est_map_hmm_given_dose.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c est_map_hmm_given_prior.cpp -o est_map_hmm_given_prior.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c genotypic_counts.cpp -o genotypic_counts.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hmm_elements.cpp -o hmm_elements.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hmm_single_parent.cpp -o hmm_single_parent.o gcc-14 -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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mappoly_init.c -o mappoly_init.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise_estimation.cpp -o pairwise_estimation.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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pairwise_estimation_rcppparallel.cpp -o pairwise_estimation_rcppparallel.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb.h:32, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel/TBB.h:10, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/RcppParallel.h:24, from pairwise_estimation_rcppparallel.cpp:41: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ 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/RcppParallel/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c read_mappoly_vcf.cpp -o read_mappoly_vcf.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o mappoly.so RcppExports.o calc_genoprob.o calc_genoprob_based_on_phased_marker_blocks.o calc_loglike_given_map.o combinatorial.o est_hmm_map_based_on_phased_mrk_blocks.o est_map_hmm_given_dose.o est_map_hmm_given_prior.o genotypic_counts.o hmm_elements.o hmm_single_parent.o mappoly_init.o pairwise_estimation.o pairwise_estimation_rcppparallel.o read_mappoly_vcf.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpG6Z4KT/R.INSTALL1f27c95486d764/mappoly/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpG6Z4KT/R.INSTALL1f27c95486d764/mappoly/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpG6Z4KT/R.INSTALL1f27c95486d764/mappoly/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-mappoly/00new/mappoly/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 ‘mappoly’ finding HTML links ... done add_marker html add_md_markers html add_mrk_at_tail_ph_list html aggregate_matrix html cache_counts_twopt html calc_genoprob html calc_genoprob_dist html calc_genoprob_error html calc_genoprob_haplo html calc_genoprob_single_parent html calc_homologprob html calc_prefpair_profiles html cat_phase html check_data_dist_sanity html check_data_dose_sanity html check_data_sanity html check_if_rf_is_possible html check_ls_phase html check_pairwise html compare_haplotypes html compare_maps html concatenate_new_marker html concatenate_ph_list html create_map html cross_simulate html detect_info_par html dist_prob_to_class html draw_cross html draw_phases html drop_marker html edit_order html elim_conf_using_two_pts html elim_equiv html elim_redundant html est_full_hmm_with_global_error html est_full_hmm_with_prior_prob html est_haplo_hmm html est_map_haplo_given_genoprob html est_pairwise_rf html est_pairwise_rf2 html est_rf_hmm html est_rf_hmm_sequential html est_rf_hmm_single_phase html est_rf_hmm_single_phase_single_parent html export_data_to_polymapR html export_map_list html export_qtlpoly html extract_map html filter_aneuploid html filter_individuals html filter_map_at_hmm_thres html filter_missing html filter_missing_ind html filter_missing_mrk html filter_non_conforming_classes html filter_segregation html find_blocks html format_rf html framework_map html generate_all_link_phase_elim_equivalent html generate_all_link_phases_elim_equivalent_haplo html genetic-mapping-functions html genotyping_global_error html get_LOD html get_cache_two_pts_from_web html get_counts html get_counts_all_phases html get_counts_single_parent html get_counts_two_parents html get_dosage_type html get_full_info_tail html get_genomic_order html get_ij html get_indices_from_selected_phases html get_ols_map html get_ph_conf_ret_sh html get_ph_list_subset html get_rf_from_list html get_rf_from_mat html get_states_and_emission_single_parent html get_submap html get_tab_mrks html get_w_m html gg_color_hue html group_mappoly html hexafake html hexafake.geno.dist html import_data_from_polymapR html import_from_updog html import_phased_maplist_from_polymapR html is.prob.data html loglike_hmm html ls_linkage_phases html make_mat_mappoly html make_pairs_mappoly html make_seq_mappoly html mappoly-color-palettes html maps.hexafake html mds_mappoly html merge_datasets html merge_maps html merge_parental_maps html mrk_chisq_test html msg html paralell_pairwise_discrete html paralell_pairwise_discrete_rcpp html paralell_pairwise_probability html parallel_block html perm_pars html perm_tot html ph_list_to_matrix html ph_matrix_to_list html plot.mappoly.homoprob html plot.mappoly.prefpair.profiles html plot_GIC html plot_compare_haplotypes html plot_genome_vs_map html plot_map_list html plot_mappoly.map2 html plot_mrk_info html plot_one_map html plot_progeny_dosage_change html poly_hmm_est html prepare_map html print_mrk html print_ph html read_fitpoly html read_geno html read_geno_csv html read_geno_prob html read_vcf html reest_rf html rev_map html rf_list_to_matrix html rf_snp_filter html sample_data html segreg_poly html select_rf html sim_cross_one_informative_parent html sim_cross_two_informative_parents html sim_homologous html solcap.dose.map html solcap.err.map html solcap.mds.map html solcap.prior.map html split_and_rephase html split_mappoly html summary_maps html table_to_mappoly html tetra.solcap html tetra.solcap.geno.dist html update_framework_map html update_map html update_missing html update_ph_list_at_hmm_thres html v_2_m 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 (mappoly)