* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘numbat’ ...
** this is package ‘numbat’ version ‘1.5.2’
** package ‘numbat’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-12) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpCuOqhD/R.INSTALL12986022108632/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
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
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
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpCuOqhD/R.INSTALL12986022108632/numbat/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpCuOqhD/R.INSTALL12986022108632/numbat/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpCuOqhD/R.INSTALL12986022108632/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_gtf_input 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)