[R/check_mrca_prior.R:27:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/check_mrca_prior.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
check_mrca_prior <- function(mrca_prior) {
^
```
[R/clock_model_to_xml_prior_distr.R:14:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/clock_model_to_xml_prior_distr.R#L14) *warning:* **no visible global function definition for ‘rln_clock_model_to_xml_mean_rate_prior’**
```r
      text <- c(text, rln_clock_model_to_xml_mean_rate_prior(clock_model)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_state.R:32:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/clock_models_to_xml_state.R#L32) *warning:* **no visible global function definition for ‘clock_model_to_xml_state’**
```r
    line_to_remove <- clock_model_to_xml_state(clock_models[[1]]) # nolint
                      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:9:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_distr.R#L9) *warning:* **no visible global function definition for ‘tree_priors_to_xml_prior_distr’**
```r
  text <- c(text, tree_priors_to_xml_prior_distr(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:10:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_distr.R#L10) *warning:* **no visible global function definition for ‘gamma_site_models_to_xml_prior_distr’**
```r
  text <- c(text, gamma_site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:11:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_distr.R#L11) *warning:* **no visible global function definition for ‘site_models_to_xml_prior_distr’**
```r
  text <- c(text, site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:27:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_operators.R#L27) *warning:* **no visible global function definition for ‘site_models_to_xml_operators’**
```r
  text <- c(text, site_models_to_xml_operators(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_run.R:23:11:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_run.R#L23) *warning:* **no visible global function definition for ‘mcmc_to_xml_run’**
```r
  text <- mcmc_to_xml_run(mcmc) # nolint beautier function
          ^~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:24:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_state.R#L24) *warning:* **no visible global function definition for ‘site_models_to_xml_state’**
```r
  text <- c(text, site_models_to_xml_state(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:33:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_state.R#L33) *warning:* **no visible global function definition for ‘tree_priors_to_xml_state’**
```r
  text <- c(text, tree_priors_to_xml_state(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_clock_models_from_names.R:5:26:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_clock_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_clock_model_from_name’**
```r
    clock_models[[i]] <- create_clock_model_from_name(clock_model_name) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc_nested_sampling.R:41:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_mcmc_nested_sampling.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
#' @aliases create_ns_mcmc create_nested_sampling_mcmc create_mcmc_nested_sampling
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc_nested_sampling.R:42:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_mcmc_nested_sampling.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
#' @export create_ns_mcmc create_nested_sampling_mcmc create_mcmc_nested_sampling
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_site_models_from_names.R:5:25:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_site_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_site_model_from_name’**
```r
    site_models[[i]] <- create_site_model_from_name(site_model_name) # nolint beautier function
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:17:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_tracelog_xml.R#L17) *warning:* **no visible global function definition for ‘tree_models_to_xml_tracelog’**
```r
  text <- c(text, tree_models_to_xml_tracelog(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:32:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_tracelog_xml.R#L32) *warning:* **no visible global function definition for ‘tree_priors_to_xml_tracelog’**
```r
  text <- c(text, tree_priors_to_xml_tracelog(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_operators_from_lines.R:13:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/extract_xml_operators_from_lines.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
  last_line <- beautier::find_last_regex_line(lines, "(<operator id=\")|(</operator>)")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_section_from_lines.R:7:12:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/extract_xml_section_from_lines.R#L7) *warning:* **no visible global function definition for ‘extract_xml_operators_from_lines’**
```r
    return(extract_xml_operators_from_lines(lines)) # nolint beautier function
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_last_xml_closing_tag_line.R:6:3:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/find_last_xml_closing_tag_line.R#L6) *warning:* **no visible global function definition for ‘find_last_regex_line’**
```r
  find_last_regex_line(lines, paste0("</", section, ">")) # nolint beautier function
  ^~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_id.R:5:9:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/get_alignment_id.R#L5) *warning:* **no visible global function definition for ‘get_file_base_sans_ext’**
```r
  id <- get_file_base_sans_ext(fasta_filename) # nolint beautier function
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:11:12:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/has_xml_opening_tag.R#L11) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
    tag <- get_xml_opening_tag(lines) # nolint
           ^~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:14:24:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/has_xml_opening_tag.R#L14) *warning:* **no visible global function definition for ‘find_first_xml_opening_tag_line’**
```r
  !beautier::is_one_na(find_first_xml_opening_tag_line(lines, section))
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:10:10:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_clock_models.R#L10) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames) # nolint beautier function
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:13:26:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_clock_models.R#L13) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(ucldstdev_distr) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:20:26:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_clock_models.R#L20) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(mean_rate_prior_distr) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_distr.R:9:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_distr.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
init_distr <- function(
^
```
[R/init_inference_model.R:39:22:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_inference_model.R#L39) *warning:* **no visible global function definition for ‘init_mrca_prior’**
```r
  inference_model <- init_mrca_prior(input_filename, inference_model)
                     ^~~~~~~~~~~~~~~
```
[R/init_mrca_prior.R:8:50:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_mrca_prior.R#L8) *warning:* **no visible global function definition for ‘get_alignment_id’**
```r
      inference_model$mrca_prior$alignment_id <- get_alignment_id(input_filename) # nolint beautier function
                                                 ^~~~~~~~~~~~~~~~
```
[R/init_mrca_prior.R:11:48:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_mrca_prior.R#L11) *warning:* **no visible global function definition for ‘get_taxa_names’**
```r
      inference_model$mrca_prior$taxa_names <- get_taxa_names(input_filename) # nolint beautier function
                                               ^~~~~~~~~~~~~~
```
[R/init_site_models.R:44:28:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L44) *warning:* **no visible global function definition for ‘get_site_model_n_params’**
```r
    param_id <- param_id + get_site_model_n_params(site_model) # nolint beautier function
                           ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:198:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L198) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(gtr_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:220:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L220) *style:* **Lines should not be more than 80 characters.**
```r
  if (!beautier::is_one_na(hky_site_model$gamma_site_model$gamma_shape_prior_distr)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:299:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L299) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(jc69_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:327:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L327) *style:* **Lines should not be more than 80 characters.**
```r
    !beautier::is_one_na(tn93_site_model$gamma_site_model$gamma_shape_prior_distr)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/interspace.R:6:11:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/interspace.R#L6) *warning:* **no visible global function definition for ‘count_trailing_spaces’**
```r
  nsni <- count_trailing_spaces(lines[1]) # nolint beautier function
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_clock_model_name.R:2:13:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_clock_model_name.R#L2) *warning:* **no visible global function definition for ‘get_clock_model_names’**
```r
  name %in% get_clock_model_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_default_mcmc.R:2:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_default_mcmc.R#L2) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  if (!is_mcmc(mcmc)) return(FALSE) # nolint beautier function
       ^~~~~~~
```
[R/is_default_mcmc.R:3:39:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_default_mcmc.R#L3) *warning:* **no visible global function definition for ‘create_mcmc’**
```r
  length(names(mcmc)) == length(names(create_mcmc()))
                                      ^~~~~~~~~~~
```
[R/is_distr.R:37:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_distr.R#L37) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
is_distr <- function(
^
```
[R/is_freq_equilibrium_name.R:4:13:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_freq_equilibrium_name.R#L4) *warning:* **no visible global function definition for ‘get_freq_equilibrium_names’**
```r
  name %in% get_freq_equilibrium_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_id.R:4:32:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_id.R#L4) *warning:* **no visible global function definition for ‘is_one_int’**
```r
  assertive::is_a_string(x) || is_one_int(x) # nolint beautier function
                               ^~~~~~~~~~
```
[R/is_init_distr.R:26:20:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_init_distr.R#L26) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(x))
                   ^~~~~~~~~~~~~~~~
```
[R/is_init_site_model.R:36:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_init_site_model.R#L36) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
is_init_gtr_site_model <- function(
^
```
[R/is_mrca_align_id_in_fasta.R:6:9:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_mrca_align_id_in_fasta.R#L6) *warning:* **no visible global function definition for ‘get_alignment_id’**
```r
  id <- get_alignment_id(fasta_filename)
        ^~~~~~~~~~~~~~~~
```
[R/is_mrca_align_ids_in_fastas.R:6:10:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_mrca_align_ids_in_fastas.R#L6) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:8:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L8) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_prior_distr)) return(FALSE) # nolint beautier function
       ^~~~~~~~
```
[R/is_site_model.R:10:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L10) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:18:10:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L18) *warning:* **no visible global function definition for ‘is_distr’**
```r
    if (!is_distr(expected_distr)) return(FALSE) # nolint beautier function
         ^~~~~~~~
```
[R/is_site_model.R:24:10:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L24) *warning:* **no visible global function definition for ‘is_param’**
```r
    if (!is_param(expected_param)) return(FALSE) # nolint beautier function
         ^~~~~~~~
```
[R/is_site_model.R:27:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L27) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:55:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L55) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
is_gtr_site_model <- function(
^
```
[R/is_site_model.R:171:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L171) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
is_tn93_site_model <- function(
^
```
[R/is_tree_prior_name.R:2:13:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_tree_prior_name.R#L2) *warning:* **no visible global function definition for ‘get_tree_prior_names’**
```r
  name %in% get_tree_prior_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~
```
[R/is_tree_prior.R:5:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_tree_prior.R#L5) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:3:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_xml.R#L3) *warning:* **no visible global function definition for ‘has_xml_opening_tag’**
```r
  if (!has_xml_opening_tag(text)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:4:7:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_xml.R#L4) *warning:* **no visible global function definition for ‘has_xml_short_closing_tag’**
```r
  if (has_xml_short_closing_tag(text)) return(TRUE) # nolint beautier function
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:5:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_xml.R#L5) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
  opening_tag <- get_xml_opening_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:6:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_xml.R#L6) *warning:* **no visible global function definition for ‘get_xml_closing_tag’**
```r
  closing_tag <- get_xml_closing_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/mcmc_to_xml_run.R:47:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/mcmc_to_xml_run.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    xml <- paste0(xml, " numInitializationAttempts=\"", mcmc$n_init_attempts, "\"")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mrca_prior_to_xml_lh_distr.R:6:34:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/mrca_prior_to_xml_lh_distr.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_prior) == 1 && is_one_na(mrca_prior)) return(NULL) # nolint beautier function
                                 ^~~~~~~~~
```
[R/mrca_priors_to_xml_state.R:6:35:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/mrca_priors_to_xml_state.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_priors) == 1 && is_one_na(mrca_priors)) return(NULL) # nolint beautier function
                                  ^~~~~~~~~
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_state.R:22:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_state.R#L22) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ac_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:25:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_state.R#L25) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ag_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:47:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_state.R#L47) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_1_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:51:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_state.R#L51) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_2_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_subst_model.R:6:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_subst_model.R#L6) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/site_model_to_xml_subst_model.R:7:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_subst_model.R#L7) *warning:* **no visible global function definition for ‘is_jc69_site_model’**
```r
  testit::assert(is_jc69_site_model(site_model))
                 ^~~~~~~~~~~~~~~~~~
```
[R/site_models_to_xml_operators.R:4:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_models_to_xml_operators.R#L4) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_tracelog.R:6:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_models_to_xml_tracelog.R#L6) *warning:* **no visible global function definition for ‘site_model_to_xml_tracelog’**
```r
    text <- c(text, site_model_to_xml_tracelog(site_model)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_operators.R:10:22:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_operators.R#L10) *warning:* **no visible global function definition for ‘get_operator_id_pre’**
```r
  operator_id_pre <- get_operator_id_pre(tree_prior) # nolint beautier function
                     ^~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:7:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L7) *warning:* **no visible global function definition for ‘bd_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, bd_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:9:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L9) *warning:* **no visible global function definition for ‘cbs_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cbs_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:11:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L11) *warning:* **no visible global function definition for ‘ccp_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, ccp_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:13:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L13) *warning:* **no visible global function definition for ‘cep_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cep_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:16:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L16) *warning:* **no visible global function definition for ‘yule_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, yule_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_distr.R:8:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_priors_to_xml_distr.R#L8) *warning:* **no visible global function definition for ‘tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_operators.R:6:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_priors_to_xml_operators.R#L6) *warning:* **no visible global function definition for ‘are_tree_priors’**
```r
  testit::assert(are_tree_priors(tree_priors)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[tests/testthat/test-are_equal_mcmcs.R:57:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/tests/testthat/test-are_equal_mcmcs.R#L57) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-check_file_and_model_agree.R:16:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/tests/testthat/test-check_file_and_model_agree.R#L16) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = create_inference_model(
                  ^
```
[tests/testthat/test-check_file_and_model_agree.R:35:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/tests/testthat/test-check_file_and_model_agree.R#L35) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = create_inference_model(
                  ^
```
[tests/testthat/test-create_treelog_xml.R:15:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/tests/testthat/test-create_treelog_xml.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
    "    <log id=\"TreeWithMetaDataLogger.t:test_output_0\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:test_output_0\"/>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


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revert


Is the extra polyfill needed? The minimum requirement of symfony is already php7.1.3


deleted to start again


Correcto


Please upload custom code of the SharePoint Foundation project phase here


Simple and effective ;)


no need to leave commented code around, just delete it and git will remember the older versions


Thanks!


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deleted to restart


class OK


IBM Cloud [toolchain](https://cloud.ibm.com/devops/toolchains/2cef73e4-1589-4b6d-ad52-2bba05849746?env_id=ibm%3Ayp%3Aeu-gb "quando-feb24b"): [Delivery Pipeline](https://cloud.ibm.com/devops/pipelines/c7530d05-4a5f-4670-8c8f-edabfb8207a0 "quando-feb24b") deployed [quando](https://github.com/andrewfstratton/quando/releases/tag/deploy-ibm-yp-eu-gb-a.stratton-sheffield.ac.uk-dev-20191113-140639 "deploy-ibm-yp-eu-gb-a.stratton-sheffield.ac.uk-dev-20191113-140639") to [dev](https://console.bluemix.net/apps/0e3846af-b18d-4b6e-9456-d83a4afc53b2?env_id=ibm:yp:eu-gb "ibm:yp:eu-gb:a.stratton@sheffield.ac.uk:dev"), including this commit


Yes, `echo "$NUXEO_CLID" > /var/lib/nuxeo/data/instance.clid` should do it.


works fine. Even better if you used a proper API for currency conversions


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TeamCity Glyssen / Glyssen pull requests [Build *.*.665.2d7987f5cbb70a7b11cdc9c29227e0453281461c](https://build.palaso.org/viewLog.html?buildId=167278&buildTypeId=Glyssen_GlyssenPullRequests2) outcome was **SUCCESS**
Summary: Tests passed: 2348, ignored: 18 Build time: 00:09:09


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"else if" is not necessary because the return exits the function. Just use "if"


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Makes it clearer that its available.


I hope this time i can get the app


looks good


ok but why not just make a new separate node, instead of replacing the body of one and readding the node name to the next


Careful about including your Discord API token in the code. Anyone can hijack any discord server this thing has access to.


you should not have to _create_ a promise here, just call `fetch().then(whatever)`


Always use braces on if statements


Thank you for pushing me into the right direction ;-) Changes have been addressed with https://github.com/danmar/cppcheck/commit/aa5c42ffc5bcf8242e326ee00953c59457ee44a0


brace on next line for vtk style


Great to see progress on manuscript. How go dem flow layers? I downloaded lots of OSM data last night in an effort to predict modes split... More soon.


> john madden

aeiou


OK


3 класса about-us__item,  text-with-icon,  text-with-icon--flower


Isn't center should be point x,y?


Thanks for letting me know.  See https://github.com/mozilla/glean/pull/475


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I meant "...NOW TORified..."


deleted


where is the Promise.all exercise?


why do we normalize here norm vector?


This is a  basic c program


looks good


I would say pass an instance of vtkCamera in here.  So more like

std::map<std::string, vtkCamera *>  that way we have access to all the paramters in camera including parallel, perspective, view angle, etc.  We may not write them all out yet, but at least we have them available shoudl we want to add them in the future.


merging back with main branch


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One fun/tricky thing is that for ordered bidicts, each of the two backing mappings does not directly associate a KT with a VT (or vice versa). Instead, the KT and VT are associated with Nodes of a linked list, which stores the ordering, and the association between KT and VT is recovered by making the two backing mappings [bidicts themselves](https://bidict.readthedocs.io/en/master/learning-from-bidict.html#id1).

That is why I used "invbyval" and "fwdbykey" here in `_DedupResult` instead of something like "oldkey" and "oldval" (respectively). For an unordered bidict, `_invm[val]` will indeed be "oldkey" (type "KT"), and `_fwdm[key]` will indeed be "oldval" (type "VT"). But for an *ordered* bidict, where `_DedupResult` is also used, these will be Nodes (`_invm[val]` will be "nodeinv", and `_fwdm[key]` will be "nodefwd"). (Compare [BidictBase._already_have](https://github.com/jab/bidict/blob/fdffda2cc/bidict/_base.py#L302) to [OrderedBidictBase._already_have](https://github.com/jab/bidict/blob/fdffda2/bidict/_orderedbase.py#L199). So the best names I could come up with here to cover both cases was "invbyval" and "fwdbykey".

I know you haven't gotten to typing ordered bidicts yet. But once you do, will this mean the type of _DedupResult need to change to something that parameterizes whether we're in the KT/VT case or the Node case, so that the "invbyval" and "fwdbykey" params can be correctly typed?

Is this all just a big sign that the code should be rewritten somehow to avoid this?


Actually I can see it, but I do not know why its not visible for you. I will send it to you in private message.


Thanks, I have to fix for esp32


this is requirements for libs


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These two cases can be merged:

```java
case "python":
case "pythonhl":
                return path + pogoClass.getName() + ".py";
```


Now could not deploy this pull request since the `now.json` file does not contain valid JSON.

	Click here to see the contents of `now.json`

{this-is-not-json}

For more information on now.json visit https://zeit.co/docs/features/configuration#now.json.


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![](https://github.trello.services/images/mini-trello-icon.png) [Schieten werkt volledig](https://trello.com/c/QT4I20WR/11-schieten-werkt-volledig)


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~~~
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~~~


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musialem dodac ze wzgledu na to ze mam Jave11, wiec akurat to nie powinno Cię dotyczyć


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Hey @wrfarina,

What do you mean by version 2?
This is my CLI version:
```
$ codeclimate --version
0.85.5
```

Can you also post your `.codeclimate.yml` here?
Are you using the `beta` channel by any chance?

I could reproduce a similar problem locally (not the same, though) by having rules that don't match the current version. So I have a few suggestions you can try:

To debug locally, you can be very specific with the tags. `.com` is now using tag [b30](https://hub.docker.com/layers/codeclimate/codeclimate-checkstyle/b30/images/sha256-36facd16f0340462eb86d8fad42558ec201efafb3ebcfd4b68ac5dc953c45f97), so you can be sure you run the same by doing:
```shell
docker pull codeclimate/codeclimate-checkstyle:b30
CODECLIMATE_DEBUG=1 codeclimate analyze --dev -e checkstyle:b30
```

Since you are not overriding any rules, simply omit the configuration and let it use the defaults. You do this by removing any `config` entry for the checkstyle plugin in the `.codeclimate.yml` file.

Let me know how this goes.


仔细读题后发现，第一种类型完全符合第二种类型的规律，所以不用分两个if语句判断yes的情况


robisz DAO ktore ma klucz Integer, a tu miales int. Nie powinno to sprawdziać problemów, ale za każdym razem byłby unboxing


brakowalo Ci defaultowych konstruktorow. Hibernate używa refleksji i potrzebuje pustego konstruktora i setterow


skad w ogole pomysl zeby robic prywatne settery?


Imagens dos Illuminatis


index


nie mozesz miec namedQuery w klasie Employee, a definiować tych metod w repozytorium dla klasy Company jak bylo wczesniej


this (very discutable) pattern is widespread among iTop. espacially in the forms handling (see for instance datamodels/2.x/itop-portal-base/portal/src/Form/ObjectFormManager.php).
Maybe you should not create surprising code thus, stand in this pattern for now, until an eventual  mass rewrite.


aah sorry, this comment is wrong, i found it later


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to w sumie moglo zostac jak bylo, ale usunalem zeby sie pozbyc konstruktora


wstrzykuj przez konstruktorh


to musisz jeszcze raz napisac. to namedQuery powinno byc w klasie Company, a nie bylo go wcale


@amai2012 @versat I added regression test: https://github.com/danmar/cppcheck/pull/2356/


niepotrzebnie uzywales mappera


I had a problem with these destructors. Memory analysis needed later.


testowy konfig zeby sie tworzylo w bazie h2, a nie laczylo do mysqla


Salut hate que d'aller plus vite , Plus ou moins debutant..


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its*


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@apancutt Invalidations have stopped working (at least for us) in v1.0.1 due to this change. URLs such as `\*` are now being encoded and passed to AWS as `\%2A`, which throws CloudFront off. It does _not_ return an error, but invalidations aren't happening either.


You want pose.ViewDirection here instead of pose.PhysicalViewDirection


[R/check_mrca_prior.R:27:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/check_mrca_prior.R#L27) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
check_mrca_prior <- function(mrca_prior) {
^
```
[R/clock_model_to_xml_prior_distr.R:14:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/clock_model_to_xml_prior_distr.R#L14) *warning:* **no visible global function definition for ‘rln_clock_model_to_xml_mean_rate_prior’**
```r
      text <- c(text, rln_clock_model_to_xml_mean_rate_prior(clock_model)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/clock_models_to_xml_state.R:32:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/clock_models_to_xml_state.R#L32) *warning:* **no visible global function definition for ‘clock_model_to_xml_state’**
```r
    line_to_remove <- clock_model_to_xml_state(clock_models[[1]]) # nolint
                      ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:9:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_distr.R#L9) *warning:* **no visible global function definition for ‘tree_priors_to_xml_prior_distr’**
```r
  text <- c(text, tree_priors_to_xml_prior_distr(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:10:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_distr.R#L10) *warning:* **no visible global function definition for ‘gamma_site_models_to_xml_prior_distr’**
```r
  text <- c(text, gamma_site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_distr.R:11:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_distr.R#L11) *warning:* **no visible global function definition for ‘site_models_to_xml_prior_distr’**
```r
  text <- c(text, site_models_to_xml_prior_distr(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_operators.R:27:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_operators.R#L27) *warning:* **no visible global function definition for ‘site_models_to_xml_operators’**
```r
  text <- c(text, site_models_to_xml_operators(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_run.R:23:11:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_run.R#L23) *warning:* **no visible global function definition for ‘mcmc_to_xml_run’**
```r
  text <- mcmc_to_xml_run(mcmc) # nolint beautier function
          ^~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:24:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_state.R#L24) *warning:* **no visible global function definition for ‘site_models_to_xml_state’**
```r
  text <- c(text, site_models_to_xml_state(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_beast2_input_state.R:33:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_beast2_input_state.R#L33) *warning:* **no visible global function definition for ‘tree_priors_to_xml_state’**
```r
  text <- c(text, tree_priors_to_xml_state(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_clock_models_from_names.R:5:26:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_clock_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_clock_model_from_name’**
```r
    clock_models[[i]] <- create_clock_model_from_name(clock_model_name) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc_nested_sampling.R:41:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_mcmc_nested_sampling.R#L41) *style:* **Lines should not be more than 80 characters.**
```r
#' @aliases create_ns_mcmc create_nested_sampling_mcmc create_mcmc_nested_sampling
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_mcmc_nested_sampling.R:42:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_mcmc_nested_sampling.R#L42) *style:* **Lines should not be more than 80 characters.**
```r
#' @export create_ns_mcmc create_nested_sampling_mcmc create_mcmc_nested_sampling
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_site_models_from_names.R:5:25:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_site_models_from_names.R#L5) *warning:* **no visible global function definition for ‘create_site_model_from_name’**
```r
    site_models[[i]] <- create_site_model_from_name(site_model_name) # nolint beautier function
                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:17:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_tracelog_xml.R#L17) *warning:* **no visible global function definition for ‘tree_models_to_xml_tracelog’**
```r
  text <- c(text, tree_models_to_xml_tracelog(site_models)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_tracelog_xml.R:32:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/create_tracelog_xml.R#L32) *warning:* **no visible global function definition for ‘tree_priors_to_xml_tracelog’**
```r
  text <- c(text, tree_priors_to_xml_tracelog(tree_priors)) # nolint beautier function
                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_operators_from_lines.R:13:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/extract_xml_operators_from_lines.R#L13) *style:* **Lines should not be more than 80 characters.**
```r
  last_line <- beautier::find_last_regex_line(lines, "(<operator id=\")|(</operator>)")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/extract_xml_section_from_lines.R:7:12:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/extract_xml_section_from_lines.R#L7) *warning:* **no visible global function definition for ‘extract_xml_operators_from_lines’**
```r
    return(extract_xml_operators_from_lines(lines)) # nolint beautier function
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/find_last_xml_closing_tag_line.R:6:3:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/find_last_xml_closing_tag_line.R#L6) *warning:* **no visible global function definition for ‘find_last_regex_line’**
```r
  find_last_regex_line(lines, paste0("</", section, ">")) # nolint beautier function
  ^~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_id.R:5:9:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/get_alignment_id.R#L5) *warning:* **no visible global function definition for ‘get_file_base_sans_ext’**
```r
  id <- get_file_base_sans_ext(fasta_filename) # nolint beautier function
        ^~~~~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:11:12:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/has_xml_opening_tag.R#L11) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
    tag <- get_xml_opening_tag(lines) # nolint
           ^~~~~~~~~~~~~~~~~~~
```
[R/has_xml_opening_tag.R:14:24:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/has_xml_opening_tag.R#L14) *warning:* **no visible global function definition for ‘find_first_xml_opening_tag_line’**
```r
  !beautier::is_one_na(find_first_xml_opening_tag_line(lines, section))
                       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:10:10:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_clock_models.R#L10) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames) # nolint beautier function
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:13:26:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_clock_models.R#L13) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(ucldstdev_distr) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_clock_models.R:20:26:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_clock_models.R#L20) *warning:* **no visible global function definition for ‘get_distr_n_params’**
```r
  param_id <- param_id + get_distr_n_params(mean_rate_prior_distr) # nolint beautier function
                         ^~~~~~~~~~~~~~~~~~
```
[R/init_distr.R:9:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_distr.R#L9) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
init_distr <- function(
^
```
[R/init_inference_model.R:39:22:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_inference_model.R#L39) *warning:* **no visible global function definition for ‘init_mrca_prior’**
```r
  inference_model <- init_mrca_prior(input_filename, inference_model)
                     ^~~~~~~~~~~~~~~
```
[R/init_mrca_prior.R:8:50:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_mrca_prior.R#L8) *warning:* **no visible global function definition for ‘get_alignment_id’**
```r
      inference_model$mrca_prior$alignment_id <- get_alignment_id(input_filename) # nolint beautier function
                                                 ^~~~~~~~~~~~~~~~
```
[R/init_mrca_prior.R:11:48:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_mrca_prior.R#L11) *warning:* **no visible global function definition for ‘get_taxa_names’**
```r
      inference_model$mrca_prior$taxa_names <- get_taxa_names(input_filename) # nolint beautier function
                                               ^~~~~~~~~~~~~~
```
[R/init_site_models.R:44:28:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L44) *warning:* **no visible global function definition for ‘get_site_model_n_params’**
```r
    param_id <- param_id + get_site_model_n_params(site_model) # nolint beautier function
                           ^~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:198:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L198) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(gtr_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:220:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L220) *style:* **Lines should not be more than 80 characters.**
```r
  if (!beautier::is_one_na(hky_site_model$gamma_site_model$gamma_shape_prior_distr)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:299:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L299) *style:* **Lines should not be more than 80 characters.**
```r
  testit::assert(beautier::is_init_gamma_site_model(jc69_site_model$gamma_site_model))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/init_site_models.R:327:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/init_site_models.R#L327) *style:* **Lines should not be more than 80 characters.**
```r
    !beautier::is_one_na(tn93_site_model$gamma_site_model$gamma_shape_prior_distr)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/interspace.R:6:11:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/interspace.R#L6) *warning:* **no visible global function definition for ‘count_trailing_spaces’**
```r
  nsni <- count_trailing_spaces(lines[1]) # nolint beautier function
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_clock_model_name.R:2:13:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_clock_model_name.R#L2) *warning:* **no visible global function definition for ‘get_clock_model_names’**
```r
  name %in% get_clock_model_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~~
```
[R/is_default_mcmc.R:2:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_default_mcmc.R#L2) *warning:* **no visible global function definition for ‘is_mcmc’**
```r
  if (!is_mcmc(mcmc)) return(FALSE) # nolint beautier function
       ^~~~~~~
```
[R/is_default_mcmc.R:3:39:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_default_mcmc.R#L3) *warning:* **no visible global function definition for ‘create_mcmc’**
```r
  length(names(mcmc)) == length(names(create_mcmc()))
                                      ^~~~~~~~~~~
```
[R/is_distr.R:37:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_distr.R#L37) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
is_distr <- function(
^
```
[R/is_freq_equilibrium_name.R:4:13:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_freq_equilibrium_name.R#L4) *warning:* **no visible global function definition for ‘get_freq_equilibrium_names’**
```r
  name %in% get_freq_equilibrium_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_id.R:4:32:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_id.R#L4) *warning:* **no visible global function definition for ‘is_one_int’**
```r
  assertive::is_a_string(x) || is_one_int(x) # nolint beautier function
                               ^~~~~~~~~~
```
[R/is_init_distr.R:26:20:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_init_distr.R#L26) *warning:* **no visible global function definition for ‘is_uniform_distr’**
```r
    testit::assert(is_uniform_distr(x))
                   ^~~~~~~~~~~~~~~~
```
[R/is_init_site_model.R:36:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_init_site_model.R#L36) *style:* **functions should have cyclomatic complexity of less than 15, this has 27.**
```r
is_init_gtr_site_model <- function(
^
```
[R/is_mrca_align_id_in_fasta.R:6:9:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_mrca_align_id_in_fasta.R#L6) *warning:* **no visible global function definition for ‘get_alignment_id’**
```r
  id <- get_alignment_id(fasta_filename)
        ^~~~~~~~~~~~~~~~
```
[R/is_mrca_align_ids_in_fastas.R:6:10:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_mrca_align_ids_in_fastas.R#L6) *warning:* **no visible global function definition for ‘get_alignment_ids_from_fasta_filenames’**
```r
  ids <- get_alignment_ids_from_fasta_filenames(fasta_filenames)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:8:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L8) *warning:* **no visible global function definition for ‘is_distr’**
```r
  if (!is_distr(x$kappa_prior_distr)) return(FALSE) # nolint beautier function
       ^~~~~~~~
```
[R/is_site_model.R:10:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L10) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:18:10:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L18) *warning:* **no visible global function definition for ‘is_distr’**
```r
    if (!is_distr(expected_distr)) return(FALSE) # nolint beautier function
         ^~~~~~~~
```
[R/is_site_model.R:24:10:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L24) *warning:* **no visible global function definition for ‘is_param’**
```r
    if (!is_param(expected_param)) return(FALSE) # nolint beautier function
         ^~~~~~~~
```
[R/is_site_model.R:27:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L27) *warning:* **no visible global function definition for ‘is_freq_equilibrium_name’**
```r
  if (!is_freq_equilibrium_name(x$freq_equilibrium)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_site_model.R:55:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L55) *style:* **functions should have cyclomatic complexity of less than 15, this has 22.**
```r
is_gtr_site_model <- function(
^
```
[R/is_site_model.R:171:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_site_model.R#L171) *style:* **functions should have cyclomatic complexity of less than 15, this has 23.**
```r
is_tn93_site_model <- function(
^
```
[R/is_tree_prior_name.R:2:13:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_tree_prior_name.R#L2) *warning:* **no visible global function definition for ‘get_tree_prior_names’**
```r
  name %in% get_tree_prior_names() # nolint beautier function
            ^~~~~~~~~~~~~~~~~~~~
```
[R/is_tree_prior.R:5:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_tree_prior.R#L5) *warning:* **no visible global function definition for ‘is_tree_prior_name’**
```r
  if (!is_tree_prior_name(x$name)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:3:8:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_xml.R#L3) *warning:* **no visible global function definition for ‘has_xml_opening_tag’**
```r
  if (!has_xml_opening_tag(text)) return(FALSE) # nolint beautier function
       ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:4:7:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_xml.R#L4) *warning:* **no visible global function definition for ‘has_xml_short_closing_tag’**
```r
  if (has_xml_short_closing_tag(text)) return(TRUE) # nolint beautier function
      ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:5:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_xml.R#L5) *warning:* **no visible global function definition for ‘get_xml_opening_tag’**
```r
  opening_tag <- get_xml_opening_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/is_xml.R:6:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/is_xml.R#L6) *warning:* **no visible global function definition for ‘get_xml_closing_tag’**
```r
  closing_tag <- get_xml_closing_tag(text) # nolint beautier function
                 ^~~~~~~~~~~~~~~~~~~
```
[R/mcmc_to_xml_run.R:47:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/mcmc_to_xml_run.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    xml <- paste0(xml, " numInitializationAttempts=\"", mcmc$n_init_attempts, "\"")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mrca_prior_to_xml_lh_distr.R:6:34:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/mrca_prior_to_xml_lh_distr.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_prior) == 1 && is_one_na(mrca_prior)) return(NULL) # nolint beautier function
                                 ^~~~~~~~~
```
[R/mrca_priors_to_xml_state.R:6:35:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/mrca_priors_to_xml_state.R#L6) *warning:* **no visible global function definition for ‘is_one_na’**
```r
  if (length(mrca_priors) == 1 && is_one_na(mrca_priors)) return(NULL) # nolint beautier function
                                  ^~~~~~~~~
```
[R/parameter_to_xml.R:13:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/parameter_to_xml.R#L13) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
parameter_to_xml <- function(
^
```
[R/site_model_to_xml_state.R:22:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_state.R#L22) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ac_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:25:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_state.R#L25) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$rate_ag_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:47:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_state.R#L47) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_1_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_state.R:51:23:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_state.R#L51) *warning:* **no visible global function definition for ‘parameter_to_xml’**
```r
      text <- c(text, parameter_to_xml(site_model$kappa_2_param)) # nolint beautier function
                      ^~~~~~~~~~~~~~~~
```
[R/site_model_to_xml_subst_model.R:6:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_subst_model.R#L6) *warning:* **no visible global function definition for ‘is_id’**
```r
  testit::assert(is_id(id))
                 ^~~~~
```
[R/site_model_to_xml_subst_model.R:7:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_model_to_xml_subst_model.R#L7) *warning:* **no visible global function definition for ‘is_jc69_site_model’**
```r
  testit::assert(is_jc69_site_model(site_model))
                 ^~~~~~~~~~~~~~~~~~
```
[R/site_models_to_xml_operators.R:4:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_models_to_xml_operators.R#L4) *warning:* **no visible global function definition for ‘are_site_models’**
```r
  testit::assert(are_site_models(site_models)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[R/site_models_to_xml_tracelog.R:6:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/site_models_to_xml_tracelog.R#L6) *warning:* **no visible global function definition for ‘site_model_to_xml_tracelog’**
```r
    text <- c(text, site_model_to_xml_tracelog(site_model)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_operators.R:10:22:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_operators.R#L10) *warning:* **no visible global function definition for ‘get_operator_id_pre’**
```r
  operator_id_pre <- get_operator_id_pre(tree_prior) # nolint beautier function
                     ^~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:7:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L7) *warning:* **no visible global function definition for ‘bd_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, bd_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:9:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L9) *warning:* **no visible global function definition for ‘cbs_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cbs_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:11:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L11) *warning:* **no visible global function definition for ‘ccp_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, ccp_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:13:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L13) *warning:* **no visible global function definition for ‘cep_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, cep_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_prior_to_xml_prior_distr.R:16:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_prior_to_xml_prior_distr.R#L16) *warning:* **no visible global function definition for ‘yule_tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, yule_tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_distr.R:8:21:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_priors_to_xml_distr.R#L8) *warning:* **no visible global function definition for ‘tree_prior_to_xml_prior_distr’**
```r
    text <- c(text, tree_prior_to_xml_prior_distr(tree_prior)) # nolint beautier function
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/tree_priors_to_xml_operators.R:6:18:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/R/tree_priors_to_xml_operators.R#L6) *warning:* **no visible global function definition for ‘are_tree_priors’**
```r
  testit::assert(are_tree_priors(tree_priors)) # nolint beautier function
                 ^~~~~~~~~~~~~~~
```
[tests/testthat/test-are_equal_mcmcs.R:57:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/tests/testthat/test-are_equal_mcmcs.R#L57) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-check_file_and_model_agree.R:16:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/tests/testthat/test-check_file_and_model_agree.R#L16) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = create_inference_model(
                  ^
```
[tests/testthat/test-check_file_and_model_agree.R:35:19:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/tests/testthat/test-check_file_and_model_agree.R#L35) *style:* **Use <-, not =, for assignment.**
```r
  inference_model = create_inference_model(
                  ^
```
[tests/testthat/test-create_treelog_xml.R:15:1:](https://github.com/ropensci/beautier/blob/eb35b8b9a5a01304f9729a932c74acef0bfbba26/tests/testthat/test-create_treelog_xml.R#L15) *style:* **Lines should not be more than 80 characters.**
```r
    "    <log id=\"TreeWithMetaDataLogger.t:test_output_0\" spec=\"beast.evolution.tree.TreeWithMetaDataLogger\" tree=\"@Tree.t:test_output_0\"/>",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


I dont't know java But i think this(copy paste 🤕 ) can Help you.
```

import android.widget.MediaController;

 YourClass{

private MediaController mMediaController = null;

try {
			mVideoView.setOnCompletionListener(this);
			mVideoView.setOnPreparedListener(this);
			mVideoView.setOnErrorListener(this);
			mVideoView.setVideoURI(videoUri);
			mMediaController = new MediaController(this);
			mMediaController.setAnchorView(mVideoView);
			mMediaController.setMediaPlayer(mVideoView);
			if (!mControls) {
				mMediaController.setVisibility(View.GONE);
			}
			mVideoView.setMediaController(mMediaController);
		} catch (Throwable t) {
			Log.d(TAG, t.toString());
		}

}

```


Modules should have a @moduledoc tag.


Yep! found the issue and fixed it.
It's just a matter of order.


BoundedElastic?


w NamedQuery nie można używać % tak po prostu. to w tym momencie dalej nie będzie działać, bo nie dodałem `%`. wiec zmatchuje dokladnie podany parametr. naprawisz to sobie uzywajac np CONCAT


Shouldn’t ‘volumes’ be replaced by a variable too?


It's kind of dumb for this case - it wants any scalars to be throwaway variables that aren't used anywhere else (even within other similar vectorized loops in the same function). See [reason code 1104 explanation](https://docs.microsoft.com/en-us/cpp/error-messages/tool-errors/vectorizer-and-parallelizer-messages?view=vs-2019#BKMK_ReasonCode110x).


indentation a bit messy, try installing "prettier"?


Successfully deployed to following URLs:

* https://finder-jbsagxy0w.now.sh
* https://finder.arnaudzg.now.sh
* https://finder-git-develop.arnaudzg.now.sh


I wonder how it behaves with large emails.


I discussed this with @steffunky , it's because it was introduced in that part of code with that commit that I suggested we change it to something better. It is still fresh and won't impact much.

But yes, there is much to change in the portal... 😅


Successfully deployed to following URLs:

* https://backyourstack-fvcadokmnw.now.sh
* https://backyourstack.now.sh
* https://backyourstack.com
* https://www.backyourstack.com


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Schema Validation Failed!
Rejecting Schema: https://firefox-ci-tc.services.mozilla.com/schemas/queue/v1/create-task-request.json#
Errors:
  * data.metadata.owner should match format "email"

---

* method:     createTask
* errorCode:  InputValidationError
* statusCode: 400
* time:       2019-11-13T14:25:57.419Z

</details>


<details>

<summary>Submitting the task to Taskcluster failed. Details</summary>

Schema Validation Failed!
Rejecting Schema: https://firefox-ci-tc.services.mozilla.com/schemas/queue/v1/create-task-request.json#
Errors:
  * data.metadata.owner should match format "email"

---

* method:     createTask
* errorCode:  InputValidationError
* statusCode: 400
* time:       2019-11-13T14:26:00.163Z

</details>


Your contribution so far is very lacking, you have to speed up.


not sure if this makes sense. Promise.all should execute something after all the promises have been resolved, here it's doing nothing.


Successfully deployed to following URLs:

* https://alexburgos-hmyyyrtl6.now.sh
* https://alexburgos-tense-coal.now.sh
* https://burgos.co
* https://alexburgos.alexburgos.now.sh
* https://alexburgos-git-master.alexburgos.now.sh


So it appears the original sin, that required this generic typing of Request/RequestHandler, was that param field inside Request was typed to either a ParamDictionary or string[] based on how the call was registered.  To try to allow typescript to properly support that that spit-personality of params, the @types/express & @types/express-serve-static-core then required all the app developers to have to specify the generic typing for Request/RequestHandler.  Doing so in customer apps has an ugly ripple-down effect of having to duplicate lots of functions that reference the Request/RequestHandler types to then have to split into separate functions of one for the default generic and another for the <string[]>.  It seems to me as a user, it would have been way less effort to have introduced a new paramArray field under the Request object so that params could be kept strictly typed to ParamDictionary and paramArray to string[], and not require the generic on Request/RequestHandler.


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~


got it


I just double-checked, `const` is irrelevant. If `SB` is declared `const` here, it still vectorizes the loop. Probably should be `const`.


whoops, missed that. Shall I add 4.0.3?


Perhaps you do the fetching and the .json() calls first, and then the DOM manipulation after those have been resolved.


wlasnie nie wiem


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
> phantomjs-prebuilt@2.1.16 install /var/aegir/projects/cms/pr703/node_modules/phantomjs-prebuilt
> node install.js

PhantomJS not found on PATH
Download already available at /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2
Verified checksum of previously downloaded file
Extracting tar contents (via spawned process)
Removing /var/aegir/projects/cms/pr703/node_modules/phantomjs-prebuilt/lib/phantom
Copying extracted folder /tmp/phantomjs/phantomjs-2.1.1-linux-x86_64.tar.bz2-extract-1573655229462/phantomjs-2.1.1-linux-x86_64 -> /var/aegir/projects/cms/pr703/node_modules/phantomjs-prebuilt/lib/phantom
Writing location.js file
Done. Phantomjs binary available at /var/aegir/projects/cms/pr703/node_modules/phantomjs-prebuilt/lib/phantom/bin/phantomjs

> core-js@2.6.9 postinstall /var/aegir/projects/cms/pr703/node_modules/core-js
> node scripts/postinstall || echo "ignore"

Thank you for using core-js ( https://github.com/zloirock/core-js ) for polyfilling JavaScript standard library!

The project needs your help! Please consider supporting of core-js on Open Collective or Patreon:
> https://opencollective.com/core-js
> https://www.patreon.com/zloirock

Also, the author of core-js ( https://github.com/zloirock ) is looking for a good job -)

added 134 packages from 190 contributors and audited 183 packages in 4.604s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/aegir/projects/cms/pr703
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov 0
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr703.ci.cms.va.gov/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Wed, 13 Nov 2019 14:27:13 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Wed, 13 Nov 2019 14:27:16 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** devshop.cms.va.gov
- **In:** 01:15


I'm having problems with the firmware version 7.45.189 of the 4345 (Linux 4.14.95), that wifi doesn't come up on the rpi3 B+.
Output of `dmesg | grep brcm`:
```
[    6.801613] brcmfmac: F1 signature read @0x18000000=0x15264345
[    6.808617] brcmfmac: brcmf_fw_map_chip_to_name: using brcm/brcmfmac43455-sdio.bin for chip 0x004345(17221) rev 0x000006
[    6.828547] usbcore: registered new interface driver brcmfmac
[    7.213063] brcmfmac: brcmf_c_preinit_dcmds: Firmware version = wl0: May  2 2019 02:46:17 version 7.45.189 (r714228 CY) FWID 01-e1db26e2
[    7.235182] brcmfmac: brcmf_c_preinit_dcmds: CLM version = API: 12.2 Data: 9.10.136 Compiler: 1.29.4 ClmImport: 1.36.3 Creation: 2019-05-02 02:31:27
[ 5249.351409] brcmfmac: brcmf_proto_bcdc_query_dcmd: brcmf_proto_bcdc_msg failed w/status -110
[ 5254.471408] brcmfmac: brcmf_dongle_scantime: Scan assoc time error (-110)
[ 5257.031443] brcmfmac: brcmf_netdev_open: failed to bring up cfg80211
[ 5259.591467] brcmfmac: brcmf_proto_bcdc_query_dcmd: brcmf_proto_bcdc_msg failed w/status -110
[ 5264.711415] brcmfmac: brcmf_dongle_scantime: Scan assoc time error (-110)
[ 5267.271413] brcmfmac: brcmf_netdev_open: failed to bring up cfg80211
```


This requires `#include <limits.h>`, otherwise this fails with GCC.


Successfully deployed to following URLs:

* https://jobify-m1tats97m.now.sh
* https://jobify-ten-rose.now.sh
* https://jobify.blogdomarcio.now.sh
* https://jobify-git-master.blogdomarcio.now.sh


This is a multi-line test comment
- With GitHub **Markdown**
- Created by [commit-comment][1]

[1]: https://github.com/peter-evans/commit-comment


Successfully deployed to following URLs:

* https://personal-website-ts-6ps5nelys.now.sh
* https://danielagg.com
* https://personal-website-ts.danielagg.now.sh
* https://personal-website-ts-git-master.danielagg.now.sh


Successfully deployed to following URLs:

* https://front-end-8weteyx8c.now.sh
* https://front-end-olive-ten.now.sh
* https://front-end.dswhitely1.now.sh
* https://front-end-git-master.dswhitely1.now.sh


ebasi testa maina


does the BinTray security token be plain text in the ci yaml...
this allows to use tha BinTray API in your behalf.

I ain't familiar with GitHub CI Tools, but I'm almost sure there should be an option of defining pipeline secret variables.
Lets say: BIN_TRAY_TOKEN=<SOME LONG TOKEN THAT ONLY HOLDER CAN SEE OR CHANGE>
and use `secure: ${BIN_TRAY_TOKEN}` in the .yaml file

also, might want to change the regenerate the token so noone will be able to use it maliciously.


`LLONG_MIN` and `LLONG_MAX` require `#include <limits.h>`, otherwise this fails with GCC.

reported to upstream here: https://github.com/Yubico/libfido2/commit/cc7631a9edd6fb56a7410bc8e6caaaed5d9f9d72#comments


Successfully deployed to following URLs:

* https://pazdora-cal-web-h09408ui7.now.sh
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* https://pazdora-cal-web.kuwak.now.sh
* https://pazdora-cal-web-git-master.kuwak.now.sh


I could not get this point, what else should be done?


Successfully deployed to following URLs:

* https://nohai-app-f9l71sy1n.now.sh
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* https://nohai-app.nohai-team.now.sh
* https://nohai-app-git-master.nohai-team.now.sh


[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 21.**
```r
check_pir_out <- function(
^
```
[R/check_sim_true_alignment_function.R:9:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/check_sim_true_alignment_function.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_true_alignment_function <- function(sim_true_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/check_sim_twin_alignment_function.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_twin_alignment_function <- function(sim_twin_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_with_std_site_model.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/create_alignment_with_std_site_model.R#L5) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/create_all_experiments.R#L24) *style:* **functions should have cyclomatic complexity of less than 15, this has 30.**
```r
create_all_experiments <- function(
^
```
[R/create_copy_twin_tree_from_true_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/create_copy_twin_tree_from_true_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_copy_twin_tree_from_true_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_bd_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/create_sim_bd_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_bd_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_yule_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/create_sim_yule_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_yule_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/est_evidences.R#L35) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
est_evidences <- function(
^
```
[R/get_alignment_sequences.R:5:3:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/get_alignment_sequences.R#L5) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/get_copy_true_alignment_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/get_copy_true_alignment_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_copy_true_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_pir_params_filenames.R:6:17:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/get_pir_params_filenames.R#L6) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_linked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_std_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/get_sim_true_alignment_with_std_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_std_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_unlinked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_std_site_model_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/get_sim_twin_alignment_with_std_site_model_function.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_std_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_run.R:22:17:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/pir_run.R#L22) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/pir_to_pics.R:10:17:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/pir_to_pics.R#L10) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/pir_to_tables.R:7:17:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/pir_to_tables.R#L7) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/select_candidate_evidences.R:25:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```
[R/sim_alignment_with_std_site_model.R:15:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_alignment_with_std_site_model.R#L15) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_linked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_true_alignment_with_linked_node_sub_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_std_site_model.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_true_alignment_with_std_site_model.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_true_alignment_with_unlinked_node_sub_site_model.R#L13) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_twin_alignment_with_same_n_mutation.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_std_site_model_raw.R:5:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_twin_alignment_with_std_site_model_raw.R#L5) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_std_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_std_site_model.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_twin_alignment_with_std_site_model.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_std_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_unlinked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/R/sim_twin_alignment_with_unlinked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_experiments_filenames.R:38:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/tests/testthat/test-get_experiments_filenames.R#L38) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:47:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/tests/testthat/test-get_pir_params_filenames.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:71:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/tests/testthat/test-get_pir_params_filenames.R#L71) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_pir_params_filenames.R:114:1:](https://github.com/richelbilderbeek/pirouette/blob/c8ee3255096524f810ba4d9dd1bc4135f8438c82/tests/testthat/test-get_pir_params_filenames.R#L114) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


Successfully deployed to following URLs:

* https://jobify-ehbvgptv2.now.sh
* https://jobify-ten-rose.now.sh
* https://jobify.blogdomarcio.now.sh
* https://jobify-git-master.blogdomarcio.now.sh


Deployment failed with the following error:

~~~
Your `package.json` file is missing a `build` property inside the `script` property.
~~~


Обнаружил ещё одну ошибку. Выясняю причины. :\


# Specs execution successful
:scroll: [View logs](http://bamboo.comnull)
### Plans updated

Bamboo specs have been successfully imported and the following plans have been updated.

Project | Plan | Build
---|---|---
[Test](http://bamboo.com/browse/TEST) | [Comment test](http://bamboo.com/browse/TEST-CTEST)  | :white_check_mark: [\#1](http://bamboo.com/browse/TEST-CTEST-1)
[New project](http://bamboo.com/browse/NEW) | [Disabled plan](http://bamboo.com/browse/NEW-DISABLED) **disabled** | :white_check_mark: [\#1](http://bamboo.com/browse/NEW-DISABLED-1)

### Deployments updated

Bamboo specs have been successfully imported and the following deployment projects have been updated.

|Deployment project |
----|
[Deployment test](http://bamboo.com/deploy/viewDeploymentProjectVersions.action?id=2162689)|


Successfully deployed to following URLs:

* https://oknaio-ifuf6zqfm.now.sh
* https://oknaio.rokealvo.now.sh
* https://oknaio-git-master.rokealvo.now.sh


Casse le projet bravo


Guys, please help. My mind is close to being blown )))
Didn't find any other place to ask.
I tried all kinds of `rawConfig`, `existingConfigMap` etc. Nothing works.
I just get blaming from helm:
Error: rpc error: code = Unknown desc = YAML parse error on fluent-bit/templates/daemonset.yaml: error converting YAML to JSON: yaml: line 61: mapping values are not allowed in this context
What I am trying to achieve is to change [outputs] section or fully `fluent-bit-output.conf`. I need it different and make it have multiple [output] sections. I can't figure out how and what should be passed.
Thank you in advance.


Successfully deployed to following URLs:

* https://csb-l9zy2-kx6x1zekf.now.sh
* https://csb-l9zy2-one-steel.now.sh
* https://redux-saga-example.now.sh
* https://saga.shawnpetros.com
* https://csb-l9zy2.shawnpetros.now.sh
* https://csb-l9zy2-git-master.shawnpetros.now.sh


@grimmxsleeper ^^


develop (punyasloka95) - x86_64-Linux-Ubuntu-18.04-gcc-7.4: Build Failed

Failures:\n

integration Test Summary
 * Passed: 1
 * Failed: 672

![Build Badge](http://img.shields.io/badge/build%20status-failing-red.png) ![Test Badge](http://img.shields.io/badge/tests%20passed-3.61%25-red.png)


Successfully deployed to following URLs:

* https://immobilienconsultingaktuell-bc1pqrdz7.now.sh
* https://immobilienconsultingaktuell.barbar.now.sh
* https://immobilienconsultingaktuell-git-master.barbar.now.sh


Right


Successfully deployed to following URLs:

* https://csb-l9zy2-hp2pi4dfr.now.sh
* https://csb-l9zy2-one-steel.now.sh
* https://redux-saga-example.now.sh
* https://saga.shawnpetros.com
* https://csb-l9zy2.shawnpetros.now.sh
* https://csb-l9zy2-git-master.shawnpetros.now.sh


Deployment failed with the following error:

~~~
You defined 1 build that did not match any source files (please ensure they are NOT defined in .nowignore):
~~~