* 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++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpozLD7n/R.INSTALL1980b06630f425/numbat/src'
g++-13 -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++-13 -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++-13 -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 '/tmp/RtmpozLD7n/R.INSTALL1980b06630f425/numbat/src'
make[1]: Entering directory '/tmp/RtmpozLD7n/R.INSTALL1980b06630f425/numbat/src'
make[1]: Leaving directory '/tmp/RtmpozLD7n/R.INSTALL1980b06630f425/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)