* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘refdb’ ...
** this is package ‘refdb’ version ‘0.1.2’
** package ‘refdb’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘refdb’
    finding HTML links ... done
    check_fields                            html  
    fields_dbs                              html  
    filter_scores                           html  
    get_ncbi_taxonomy                       html  
    igraph_from_taxo                        html  
    make_ncbi_table                         html  
    ncbi_taxo_rank                          html  
    process_geo_ncbi                        html  
    refdb-package                           html  
    refdb_check_seq_conflict                html  
    refdb_check_seq_homogeneity             html  
    refdb_check_tax_conflict                html  
    refdb_check_tax_typo                    html  
    refdb_clean_seq_crop_primers            html  
    refdb_clean_seq_remove_gaps             html  
    refdb_clean_seq_remove_sideN            html  
    refdb_clean_tax_NA                      html  
    refdb_clean_tax_harmonize_nomenclature
                                            html  
    refdb_clean_tax_remove_blank            html  
    refdb_clean_tax_remove_extra            html  
    refdb_clean_tax_remove_subsp            html  
    refdb_clean_tax_remove_uncertainty      html  
    refdb_export_dada2                      html  
    refdb_export_idtaxa                     html  
    refdb_export_mothur                     html  
    refdb_export_utax                       html  
    refdb_fill_tax_downstream               html  
    refdb_fill_tax_upstream                 html  
    refdb_filter_ref_scope                  html  
    refdb_filter_seq_ambiguous              html  
    refdb_filter_seq_duplicates             html  
    refdb_filter_seq_homopolymers           html  
    refdb_filter_seq_length                 html  
    refdb_filter_seq_primer                 html  
    refdb_filter_seq_stopcodon              html  
    refdb_filter_tax_na                     html  
    refdb_filter_tax_precision              html  
    refdb_get_fields                        html  
    refdb_import_NCBI                       html  
    refdb_merge                             html  
    refdb_plot_map                          html  
    refdb_plot_seqlen_hist                  html  
    refdb_plot_tax_barplot                  html  
    refdb_plot_tax_tree                     html  
    refdb_plot_tax_treemap                  html  
    refdb_report                            html  
    refdb_sample_tax                        html  
    refdb_set_fields                        html  
    refdb_set_ncbitax                       html  
    refdb_write_fields                      html  
    valid_taxo_rank                         html  
    xml_extract                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (refdb)