* 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 14.2.0-8) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpy0GMQt/R.INSTALL1fe82e952fe3c/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<T>& 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<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
544 | return (atomic<T>&)t;
| ^~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& 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<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
544 | return (atomic<T>&)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/Rtmpy0GMQt/R.INSTALL1fe82e952fe3c/mappoly/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpy0GMQt/R.INSTALL1fe82e952fe3c/mappoly/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpy0GMQt/R.INSTALL1fe82e952fe3c/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)