* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘onemap’ ...
** this is package ‘onemap’ version ‘3.2.2’
** package ‘onemap’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’
using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0dV6x3/R.INSTALL3b213c640b4b42/onemap/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 find_bins.cpp -o find_bins.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 hmm_bc.cpp -o hmm_bc.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 hmm_f2.cpp -o hmm_f2.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 hmm_out.cpp -o hmm_out.o
gcc-14 -std=gnu23 -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 -Wstrict-prototypes -pedantic -mtune=native -c onemap_init.c -o onemap_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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c out_est.cpp -o out_est.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 twopts_bc.cpp -o twopts_bc.o
twopts_bc.cpp: In function ‘Rcpp::NumericMatrix est_rf_bc(Rcpp::NumericVector, int, int, int, int)’:
twopts_bc.cpp:117:27: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
117 | if(k_sub.size() != n_ind || k1_sub.size() != n_ind) {
| ~~~~~~~~~~~~~^~~~~~~~
twopts_bc.cpp:117:53: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
117 | if(k_sub.size() != n_ind || k1_sub.size() != n_ind) {
| ~~~~~~~~~~~~~~^~~~~~~~
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 twopts_out.cpp -o twopts_out.o
twopts_out.cpp: In function ‘Rcpp::List est_rf_out(Rcpp::NumericVector, int, Rcpp::IntegerVector, int, int)’:
twopts_out.cpp:122:21: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
122 | if(k_sub.size() != n_ind || k1_sub.size() != n_ind) {
| ~~~~~~~~~~~~~^~~~~~~~
twopts_out.cpp:122:47: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
122 | if(k_sub.size() != n_ind || k1_sub.size() != n_ind) {
| ~~~~~~~~~~~~~~^~~~~~~~
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 utils.cpp -o utils.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o onemap.so find_bins.o hmm_bc.o hmm_f2.o hmm_out.o onemap_init.o out_est.o twopts_bc.o twopts_out.o utils.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0dV6x3/R.INSTALL3b213c640b4b42/onemap/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0dV6x3/R.INSTALL3b213c640b4b42/onemap/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0dV6x3/R.INSTALL3b213c640b4b42/onemap/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-onemap/00new/onemap/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘onemap’
finding HTML links ... done
Bonferroni_alpha html
acum html
add_marker html
add_redundants html
check_data html
check_twopts html
combine_onemap html
compare html
create_data_bins html
create_dataframe_for_plot_outcross html
create_depths_profile html
create_probs html
draw_map html
draw_map2 html
drop_marker html
edit_order_onemap html
empty_onemap_obj html
est_map_hmm_out html
export_mappoly_genoprob html
export_viewpoly html
extract_depth html
filter_2pts_gaps html
filter_missing html
filter_prob html
find_bins html
generate_overlapping_batches html
group html
group_seq html
group_upgma html
haldane html
keep_only_selected_mks html
kosambi html
load_onemap_sequences html
make_seq html
map html
map_avoid_unlinked html
map_overlapping_batches html
map_save_ram html
mapmaker_example_f2 html
marker_type html
mds_onemap html
onemap_example_bc html
onemap_example_f2 html
onemap_example_out html
onemap_example_riself html
onemap_read_vcfR html
ord_by_geno html
order_seq html
parents_haplotypes html
pick_batch_sizes html
plot.group.upgma html
plot.onemap html
plot.onemap_progeny_haplotypes html
plot.onemap_progeny_haplotypes_counts html
plot.onemap_segreg_test html
plot_by_segreg_type html
plot_genome_vs_cm html
print.compare html
print.group html
print.group.upgma html
print.group_seq html
print.onemap html
print.onemap_bin html
print.onemap_segreg_test html
print.order html
print.rf_2pts html
print.sequence html
print.try html
progeny_haplotypes html
progeny_haplotypes_counts html
rcd html
read_mapmaker html
read_onemap html
record html
remove_inds html
rf_2pts html
rf_graph_table html
rf_snp_filter_onemap html
ripple_seq html
rm_dupli_mks html
save_onemap_sequences html
seeded_map html
select_segreg html
seq_by_type html
seriation html
set_map_fun html
simu_example_bc html
simu_example_f2 html
simu_example_out html
sort_by_pos html
split_2pts html
split_onemap html
suggest_lod html
summary_maps_onemap html
test_segregation html
test_segregation_of_a_marker html
try_seq html
try_seq_by_seq html
ug html
vcf2raw html
vcf_example_bc html
vcf_example_f2 html
vcf_example_out html
vcf_example_riself html
write_map html
write_onemap_raw 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 (onemap)