* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘minSNPs’ ...
** this is package ‘minSNPs’ version ‘0.2.0’
** package ‘minSNPs’ 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 ‘minSNPs’
    finding HTML links ... done
    binomial_naive_bayes                    html  
    branch_and_search                       html  
    cal_fn                                  html  
    cal_fp                                  html  
    cal_met_snp                             html  
    calculate_mcc                           html  
    calculate_mcc_multi                     html  
    calculate_percent                       html  
    calculate_simpson                       html  
    calculate_simpson_by_group              html  
    calculate_state                         html  
    calculate_variant_within_group          html  
    check_fasta_meta_mapping                html  
    check_meta_target                       html  
    check_multistate                        html  
    check_percent                           html  
    coef.binomial_naive_bayes               html  
    combine_fastq_search_result             html  
    combine_search_string_result            html  
    combine_search_string_result_from_files
                                            html  
    combine_search_string_result_from_list
                                            html  
    estimate_coverage                       html  
    extend_length                           html  
    find_optimised_snps                     html  
    flag_allele                             html  
    flag_position                           html  
    full_merge                              html  
    full_merge_1                            html  
    generate_kmer_search_string             html  
    generate_kmers                          html  
    generate_pattern                        html  
    generate_prioritisation                 html  
    generate_snp_search_string              html  
    get_all_process_methods                 html  
    get_binomial_tables                     html  
    get_metric_fun                          html  
    get_positions_to_search                 html  
    get_snps_set                            html  
    get_usual_length                        html  
    identify_overlaps                       html  
    infer_from_combined                     html  
    iterate_merge                           html  
    iterate_through                         html  
    map_profile_to_target                   html  
    match_count                             html  
    mcc_calculation                         html  
    merge_fasta                             html  
    output_parsed                           html  
    output_result                           html  
    output_to_files                         html  
    parse_group_mcc                         html  
    parse_group_mcc_multi                   html  
    predict.binomial_naive_bayes            html  
    predict_balk                            html  
    print.binomial_naive_bayes              html  
    process_allele                          html  
    process_kmer_result                     html  
    process_result_file                     html  
    process_snp_result                      html  
    profile_to_group_result                 html  
    read_fasta                              html  
    read_sequences_from_fastq               html  
    remove_dup_isolate                      html  
    remove_snp_conflict                     html  
    resolve_IUPAC_missing                   html  
    reverse_complement                      html  
    scramble_sequence                       html  
    search_from_fastq_reads                 html  
    search_from_reads                       html  
    select_n_set_i_depth                    html  
    sequence_reads_match_count              html  
    summarise_result                        html  
    summary.binomial_naive_bayes            html  
    train_balk                              html  
    transform_snp                           html  
    translate_position                      html  
    view_mcc                                html  
    view_mcc_multi                          html  
    view_percent                            html  
    view_simpson                            html  
    write_fasta                             html  
** 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 (minSNPs)