* 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++-14 (Debian 14.2.0-8) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpetpOH8/R.INSTALL3e7acb449ae201/sigminer/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 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/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c calc_cosine.cpp -o calc_cosine.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 get_intersect_size.cpp -o get_intersect_size.o
g++-14 -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 '/home/hornik/tmp/scratch/RtmpetpOH8/R.INSTALL3e7acb449ae201/sigminer/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpetpOH8/R.INSTALL3e7acb449ae201/sigminer/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpetpOH8/R.INSTALL3e7acb449ae201/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)