* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘sigminer’ ...
** package ‘sigminer’ 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/RtmpfwaQek/R.INSTALL1b1b507a4a8b0a/sigminer/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/usr/local/include -D_FORTIFY_SOURCE=3 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calc_cosine.cpp -o calc_cosine.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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c get_intersect_size.cpp -o get_intersect_size.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o sigminer.so RcppExports.o calc_cosine.o get_intersect_size.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpfwaQek/R.INSTALL1b1b507a4a8b0a/sigminer/src'
make[1]: Entering directory '/tmp/RtmpfwaQek/R.INSTALL1b1b507a4a8b0a/sigminer/src'
make[1]: Leaving directory '/tmp/RtmpfwaQek/R.INSTALL1b1b507a4a8b0a/sigminer/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-sigminer/00new/sigminer/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to 'sqrt'
** help
*** installing help indices
converting help for package ‘sigminer’
finding HTML links ... done
CN.features html
CopyNumber-class html
MAF-class html
add_h_arrow html
add_labels html
bp html
centromeres.T2T html
centromeres.hg19 html
centromeres.hg38 html
centromeres.mm10 html
centromeres.mm9 html
chromsize.T2T html
chromsize.hg19 html
chromsize.hg38 html
chromsize.mm10 html
chromsize.mm9 html
cosine html
cytobands.T2T html
cytobands.hg19 html
cytobands.hg38 html
cytobands.mm10 html
cytobands.mm9 html
enrich_component_strand_bias html
get_Aneuploidy_score html
get_adj_p html
get_bayesian_result html
get_cn_freq_table html
get_cn_ploidy html
get_genome_annotation html
get_group_comparison html
get_groups html
get_intersect_size html
get_pLOH_score html
get_shannon_diversity_index html
get_sig_cancer_type_index html
get_sig_db html
get_sig_exposure html
get_sig_feature_association html
get_sig_rec_similarity html
get_sig_similarity html
get_tidy_association html
group_enrichment html
group_enrichment2 html
handle_hyper_mutation html
hello html
output_bootstrap html
output_fit html
output_sig html
output_tally html
pipe html
read_copynumber html
read_copynumber_ascat html
read_copynumber_seqz html
read_maf html
read_sv_as_rs html
read_vcf html
read_xena_variants html
report_bootstrap_p_value html
same_size_clustering html
scoring html
show_catalogue html
show_cn_circos html
show_cn_components html
show_cn_distribution html
show_cn_features html
show_cn_freq_circos html
show_cn_group_profile html
show_cn_profile html
show_cor html
show_cosmic html
show_cosmic_sig_profile html
show_group_comparison html
show_group_distribution html
show_group_enrichment html
show_group_mapping html
show_groups html
show_sig_bootstrap html
show_sig_consensusmap html
show_sig_exposure html
show_sig_feature_corrplot html
show_sig_fit html
show_sig_profile html
show_sig_profile_heatmap html
show_sig_profile_loop html
sig_auto_extract html
sig_convert html
sig_estimate html
sig_extract html
sig_fit html
sig_fit_bootstrap html
sig_fit_bootstrap_batch html
sig_operation html
sig_tally html
sig_unify_extract html
sigminer-package html
sigprofiler html
simulated_catalogs html
simulation html
subset.CopyNumber html
tidyeval html
transcript.T2T html
transcript.hg19 html
transcript.hg38 html
transcript.mm10 html
transcript.mm9 html
transform_seg_table html
use_color_style html
*** copying figures
** 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 (sigminer)