* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘immunarch’ ...
** package ‘immunarch’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-5) 13.2.0’
make[1]: Entering directory '/tmp/Rtmp7MKBI6/R.INSTALL2b0bb148d6b6b/immunarch/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 fill_functions.cpp -o fill_functions.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o immunarch.so RcppExports.o fill_functions.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp7MKBI6/R.INSTALL2b0bb148d6b6b/immunarch/src'
make[1]: Entering directory '/tmp/Rtmp7MKBI6/R.INSTALL2b0bb148d6b6b/immunarch/src'
make[1]: Leaving directory '/tmp/Rtmp7MKBI6/R.INSTALL2b0bb148d6b6b/immunarch/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-immunarch/00new/immunarch/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 ‘immunarch’
    finding HTML links ... done
    aa_properties                           html  
    aa_table                                html  
    add_class                               html  
    apply_symm                              html  
    bcrdata                                 html  
    bunch_translate                         html  
    check_distribution                      html  
    coding                                  html  
    finding level-2 HTML links ... done

    dbAnnotate                              html  
    dbLoad                                  html  
    dot-quant_column_choice                 html  
    entropy                                 html  
    fixVis                                  html  
    geneUsage                               html  
    geneUsageAnalysis                       html  
    gene_segments                           html  
    gene_stats                              html  
    getKmers                                html  
    group_from_metadata                     html  
    has_class                               html  
    immdata                                 html  
    immunr_data_format                      html  
    immunr_hclust                           html  
    immunr_pca                              html  
    inc_overlap                             html  
    matrixdiagcopy                          html  
    pubRep                                  html  
    pubRepApply                             html  
    pubRepFilter                            html  
    pubRepStatistics                        html  
    public_matrix                           html  
    repAlignLineage                         html  
    repClonalFamily                         html  
    repClonality                            html  
    repDiversity                            html  
    repExplore                              html  
    repFilter                               html  
    repGermline                             html  
    repLoad                                 html  
    repOverlap                              html  
    repOverlapAnalysis                      html  
    repSample                               html  
    repSave                                 html  
    repSomaticHypermutation                 html  
    scdata                                  html  
    select_barcodes                         html  
    select_clusters                         html  
    seqCluster                              html  
    seqDist                                 html  
    set_pb                                  html  
    spectratype                             html  
    split_to_kmers                          html  
    switch_type                             html  
    top                                     html  
    trackClonotypes                         html  
    vis                                     html  
    vis.clonal_family                       html  
    vis.clonal_family_tree                  html  
    vis.immunr_chao1                        html  
    vis.immunr_clonal_prop                  html  
    vis.immunr_dynamics                     html  
    vis.immunr_exp_vol                      html  
    vis.immunr_gene_usage                   html  
    vis.immunr_hclust                       html  
    vis.immunr_inc_overlap                  html  
    vis.immunr_kmeans                       html  
    vis.immunr_kmer_table                   html  
    vis.immunr_mds                          html  
    vis.immunr_ov_matrix                    html  
    vis.immunr_public_repertoire            html  
    vis.immunr_public_statistics            html  
    vis.step_failure_ignored                html  
    vis_bar                                 html  
    vis_box                                 html  
    vis_circos                              html  
    vis_heatmap                             html  
    vis_heatmap2                            html  
    vis_hist                                html  
    vis_immunr_kmer_profile_main            html  
    vis_public_clonotypes                   html  
    vis_public_frequencies                  html  
    vis_textlogo                            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 (immunarch)