[R/alignment_params_to_posterior_trees.R:78:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/alignment_params_to_posterior_trees.R#L78) *style:* **Lines should not be more than 80 characters.**
```r
  # if (beautier::is_one_na(experiment$inference_model$mcmc$tracelog$filename)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_init_pir_params.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/check_init_pir_params.R#L2) *warning:* **no visible global function definition for ‘check_pir_params’**
```r
  check_pir_params(pir_params)
  ^~~~~~~~~~~~~~~~
```
[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
check_pir_out <- function(
^
```
[R/check_sim_true_alignment_function.R:9:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/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/317a8ffe00ce33c8020864c20701d0b23bc938d0/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/check_sim_twin_alignment_function.R:20:5:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/check_sim_twin_alignment_function.R#L20) *style:* **Commented code should be removed.**
```r
  # n_args <- stringr::str_count(string = arguments, pattern = ",") + 1
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/check_sim_twin_alignment_function.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
  #     "'sim_twin_alignment_function' must be a function with two arguments. \n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:23:21:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/check_sim_twin_alignment_function.R#L23) *warning:* **no visible global function definition for ‘get_default_sim_true_alignment_function’**
```r
  true_alignment <- get_default_sim_true_alignment_function()(twin_phylogeny)
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:56:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/check_sim_twin_alignment_function.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
        "'sim_twin_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_params.R:53:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment_params.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
  sim_true_alignment_function = pirouette::get_default_sim_true_alignment_function(),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_params.R:87:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment_params.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
  sim_true_alignment_function = pirouette::get_default_sim_true_alignment_function(),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:12:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment.R#L12) *warning:* **local variable ‘max_n_mutations’ assigned but may not be used**
```r
  max_n_mutations <- n_taxa * n_nucleotides
  ^~~~~~~~~~~~~~~
```
[R/create_alignment.R:31:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment.R#L31) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/create_alignment.R:68:9:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment.R#L68) *style:* **Commented code should be removed.**
```r
    #   alignment_params = alignment_params
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:99:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment.R#L99) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:116:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment.R#L116) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_twin_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:145:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment.R#L145) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:168:69:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment.R#L168) *style:* **Commas should always have a space after.**
```r
      "Actual 'class(alignment_phydat)': ", class(alignment_phydat)," \n",
                                                                    ^
```
[R/create_alignment.R:169:55:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_alignment.R#L169) *style:* **Commas should always have a space after.**
```r
      "Actual 'alignment_phydat': ", alignment_phydat," \n"
                                                      ^
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/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/317a8ffe00ce33c8020864c20701d0b23bc938d0/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:21:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_sim_bd_twin_tree_function.R#L21) *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:21:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_sim_yule_twin_tree_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_yule_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_twin_alignment_with_standard_site_model.R:14:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_twin_alignment_with_standard_site_model.R#L14) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/create_twin_alignment_with_standard_site_model.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/create_twin_alignment_with_standard_site_model.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_twin_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/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_n_taxa.R:14:5:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_alignment_n_taxa.R#L14) *style:* **Commented code should be removed.**
```r
  # length(labels(alignment))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_sequences.R:5:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_alignment_sequences.R#L5) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/get_default_sim_true_alignment_function.R:3:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_default_sim_true_alignment_function.R#L3) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_default_sim_true_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_default_sim_twin_alignment_function.R:4:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_default_sim_twin_alignment_function.R#L4) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_default_sim_twin_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_pir_params_filenames.R:6:17:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/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:15:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L15) *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_standard_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_sim_true_alignment_with_standard_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L12) *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:2:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L2) *warning:* **no visible binding for global variable ‘sim_twin_alignment_with_same_n_mutation’**
```r
  sim_twin_alignment_with_same_n_mutation
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L28) *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_standard_site_model_function.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_sim_twin_alignment_with_standard_site_model_function.R#L2) *warning:* **no visible binding for global variable ‘create_twin_alignment_with_standard_site_model’**
```r
  create_twin_alignment_with_standard_site_model
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_standard_site_model_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/get_sim_twin_alignment_with_standard_site_model_function.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_standard_site_model_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_run_true_tree.R:8:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/pir_run_true_tree.R#L8) *warning:* **no visible global function definition for ‘check_init_pir_params’**
```r
  check_init_pir_params(pir_params)
  ^~~~~~~~~~~~~~~~~~~~~
```
[R/pir_run.R:24:17:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/pir_run.R#L24) *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/317a8ffe00ce33c8020864c20701d0b23bc938d0/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/317a8ffe00ce33c8020864c20701d0b23bc938d0/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/317a8ffe00ce33c8020864c20701d0b23bc938d0/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_true_alignment_with_linked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/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_linked_node_sub_site_model.R:39:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/sim_true_alignment_with_linked_node_sub_site_model.R#L39) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/sim_true_alignment_with_standard_site_model.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:27:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/sim_true_alignment_with_standard_site_model.R#L27) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/sim_true_alignment_with_unlinked_node_sub_site_model.R#L12) *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_true_alignment.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/sim_true_alignment.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:4:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L4) *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:15:3:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/sim_twin_alignment_with_same_n_mutation.R#L15) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/R/sim_twin_alignment_with_same_n_mutation.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_experiments.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_experiments.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
  cand_experiment_1$inference_model$mcmc <- cand_experiment_2$inference_model$mcmc
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:77:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_true_alignment_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(true_phylogeny = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:79:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_true_alignment_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(true_phylogeny = "irrelevant") { }
                                                                              ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_true_alignment_function.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:75:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_true_alignment_function.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:77:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_true_alignment_function.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:9:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_true_alignment_function.R#L37) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:25:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_true_alignment_function.R#L37) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:39:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_true_alignment_function.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_alignment_function.R:21:62:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:21:64:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:27:62:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L27) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:27:64:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L27) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:9:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "irrelevant" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:24:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "irrelevant" }
                       ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:45:9:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L45) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:45:25:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L45) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:47:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_alignment_function.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:66:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(one_too, many_arguments) { }
                                                                 ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:68:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(one_too, many_arguments) { }
                                                                   ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:74:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
                                                                         ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:90:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
                                                                                ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_tree_function' must be a function with one argument called 'true_phylogeny'"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:72:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                       ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:88:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                                ^
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-create_error_measure_params.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
      list.files(dirname(experiment$errors_filename), pattern = basename(experiment$errors_filename))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_twin_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-create_twin_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:115:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-get_alignment_n_taxa.R#L115) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:116:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-get_alignment_n_taxa.R#L116) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_experiments_filenames.R:10:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-get_experiments_filenames.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_experiments_filenames.R:32:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-get_experiments_filenames.R#L32) *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:14:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-get_pir_params_filenames.R#L14) *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:41:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-get_pir_params_filenames.R#L41) *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:65:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-get_pir_params_filenames.R#L65) *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:107:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-get_pir_params_filenames.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-pir_run.R:125:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-pir_run.R#L125) *style:* **Lines should not be more than 80 characters.**
```r
  twin_alignment <- readLines(pir_params$twinning_params$twin_alignment_filename)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_alignment_with_n_mutations.R:86:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-sim_alignment_with_n_mutations.R#L86) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-sim_true_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment.R:33:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-sim_true_alignment.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
    sim_true_alignment_function = get_sim_true_alignment_with_linked_node_sub_site_model_function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_true_alignment.R:66:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-sim_true_alignment.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    sim_true_alignment_function = get_sim_true_alignment_with_unlinked_node_sub_site_model_function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_true_alignment.R:95:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-sim_true_alignment.R#L95) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R:19:1:](https://github.com/richelbilderbeek/pirouette/blob/317a8ffe00ce33c8020864c20701d0b23bc938d0/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```


All those methods can be override

El mar., 5 nov. 2019 9:22, Rubén Zorrilla <notifications@github.com>
escribió:

> We discussed about it and we decided to create a new class, mainly due to
> the completely different approach used in the kinematics calculation.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/KratosMultiphysics/Kratos/commit/41054d852e1620d5473f11061f729ab092942415?email_source=notifications&email_token=AEYQZABAXKB5ADQIUDN5H4TQSEUMRA5CNFSM4JIVHNEKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBCEWYF#commitcomment-35805957>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AEYQZAE75Q6JUO45YXHKDKLQSEUMRANCNFSM4JIVHNEA>
> .
>


I know, it was (or still is?) incorrectly mentioned in the guide. I'm not sure when the guide was changed the last time. But as said, I'm not much of a Google Docs fan.


That method can be override too

El mar., 5 nov. 2019 9:29, Rubén Zorrilla <notifications@github.com>
escribió:

> Aside of the fact that the DOFs are not the same.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/KratosMultiphysics/Kratos/commit/41054d852e1620d5473f11061f729ab092942415?email_source=notifications&email_token=AEYQZAD7L7VKFI3PO3WALRTQSEUNVA5CNFSM4JIVHNEKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBCEWYJ#commitcomment-35805961>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AEYQZAFBTCUIIRFD4LSFXOLQSEUNVANCNFSM4JIVHNEA>
> .
>


コードレビュー/04_上級/プログラム作成問題：上級編/20191013_135723681/ネームバトラー【上級編】(学習4、5、6)/5.職業（僧侶）を追加/Priest.java

55～58行目までインデントを揃えましょう。
else文内なので、elseよりインデントを下げましょう。


We're now reading from the urandom device which works quite well.


Hey committed


this breaks use of QGIS API when it's installed.
Because qgsfield_p.h is include in qgsfield.h


Is this a typo? `aquire` vs `acquire`?


I spoke yesterday with Riccardo and the argument was for clarity. Certainly
I am not in favor. In any case I would move common implémentations to
static utilities in order to avoid code duplication at least.

El mar., 5 nov. 2019 9:22, Rubén Zorrilla <notifications@github.com>
escribió:

> We discussed about it and we decided to create a new class, mainly due to
> the completely different approach used in the kinematics calculation.
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
> <https://github.com/KratosMultiphysics/Kratos/commit/41054d852e1620d5473f11061f729ab092942415?email_source=notifications&email_token=AEYQZABAXKB5ADQIUDN5H4TQSEUMRA5CNFSM4JIVHNEKYY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBCEWYF#commitcomment-35805957>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AEYQZAE75Q6JUO45YXHKDKLQSEUMRANCNFSM4JIVHNEA>
> .
>


so you want me to replace a .jar with html redirect?


この場所にあると、回復した場合でもダメージ表記がされてしまいます。
通常攻撃した場合のみ表示させるようにしましょう。


这里应该翻译成“上一次运行”，容器崩溃后环境不会改变（重新拉起而不是删掉重建），不能算是“以前的容器”。


для сессий, уберу ее сегодня/завтра


What happens if `resolvePhase == SUPER_TYPES`? Is is possible we activate class supertypes resolve twice? (once from here and once from regular supertype resolver)


@pylessard After tried with your new change, like below:
`
   from udsoncan.Request import Request
   from udsoncan import services
   req = Request(service = services.DiagnosticSessionControl, subfunction=0)
   with client.payload_override(bytes.fromhex("1003")):
       response = client.send_request(req)
       print(response)`
it works.
But if user had to first use Request, then with client.payload_override, then client.send_request,
if this order is correct, I have to say this is not easy for user to use.
is it possible to change this to one function call?


Successfully deployed to following URLs:

* https://w4ctechgithubio-82sucnqph.now.sh
* https://98say.now.sh
* https://w4ctechgithubio.w4ctech.now.sh
* https://w4ctechgithubio-git-master.w4ctech.now.sh


Successfully deployed to following URLs:

* https://nuxt-typescript-vuetify-jzc800itp.now.sh
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* https://nuxt-typescript-vuetify-git-master.justhannes.now.sh


zzzzzzzzzzzzzzzzzzzzzzzzzzzzzz


private headers should not be included in public headers. This defeats the purpose.
If possible move the include to the cpp file.
If not possible move the _p.h file to `QGIS_CORE_HDRS` for now


Successfully deployed to following URLs:

* https://reacnetgenerator-pd0bw3fsm.now.sh
* https://reacnetgenerator.tongzhugroup.now.sh
* https://reacnetgenerator-git-master.tongzhugroup.now.sh


May be `WithLoopProtection` or `WithRecursionProtection` or something like...


please use imperative present tense for verbs. Yes I had to look it up myself xD
What I mean is: Referring to the commit message, please use "add" instead of "adding". The commit message is supposed to say what this commit does.

Besides, adding a footer it is not :>


Commit reverted.


this group can be deleted


Successfully deployed to following URLs:

* https://tycdwaoms-76m2zvr3d.now.sh
* https://slides.tycdwaoms.mrtnvh.com
* https://mot.mrtnvh.com
* https://tycdwaoms.mrtnvh.now.sh
* https://tycdwaoms-git-master.mrtnvh.now.sh


Successfully deployed to following URLs:

* https://communityqiskitorg-aivz7tmyb.now.sh
* https://communityqiskitorg.neosalvador.now.sh
* https://communityqiskitorg-git-master.neosalvador.now.sh


Hi I need some information and some help. Im not a programmer or know a lot about computers. I’d like to know how someone can broadcast or stream my home. There is a hud here and a lot of other things going on that I’m trying to figure out. I was told to look up this site,glint/glider/grit/ hub/hud and quantum physics. Is there anyone available to help me on this?


see above


all the groups following this line are redundant


@mateumann I've checked that all CGenNode variations has not common fields and it should not mess up anything.


Successfully deployed to following URLs:

* https://accounting-system-idqsucf2v.now.sh
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* https://accounting-system-git-master.dksami.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):
~~~


This commit has been mentioned on **Discourse Meta**. There might be relevant details there:

https://meta.discourse.org/t/moving-messages-to-existing-topics-is-broken-on-mobile/132625/4


Are there any such broken files in the wild?


why this function is duplicated?


@loumalouomega as i told you yesterday, i do not want to derive from the same element. we considered it but we would have to override ALL the auxiliary functions and we would get no advantage at all.

about the possibility of using static functions in the implementation, i think it could be a fair discussion but which is definitely out of scope for this PR


[R/alignment_params_to_posterior_trees.R:78:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/alignment_params_to_posterior_trees.R#L78) *style:* **Lines should not be more than 80 characters.**
```r
  # if (beautier::is_one_na(experiment$inference_model$mcmc$tracelog$filename)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_init_pir_params.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/check_init_pir_params.R#L2) *warning:* **no visible global function definition for ‘check_pir_params’**
```r
  check_pir_params(pir_params)
  ^~~~~~~~~~~~~~~~
```
[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/check_pir_out.R#L17) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
check_pir_out <- function(
^
```
[R/check_sim_true_alignment_function.R:9:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/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/bdddec10668953ea8c65decfe0863a95c878b3e7/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/check_sim_twin_alignment_function.R:20:5:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/check_sim_twin_alignment_function.R#L20) *style:* **Commented code should be removed.**
```r
  # n_args <- stringr::str_count(string = arguments, pattern = ",") + 1
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/check_sim_twin_alignment_function.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
  #     "'sim_twin_alignment_function' must be a function with two arguments. \n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:23:21:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/check_sim_twin_alignment_function.R#L23) *warning:* **no visible global function definition for ‘get_default_sim_true_alignment_function’**
```r
  true_alignment <- get_default_sim_true_alignment_function()(twin_phylogeny)
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:56:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/check_sim_twin_alignment_function.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
        "'sim_twin_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_params.R:53:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment_params.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
  sim_true_alignment_function = pirouette::get_default_sim_true_alignment_function(),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_params.R:87:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment_params.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
  sim_true_alignment_function = pirouette::get_default_sim_true_alignment_function(),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:12:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment.R#L12) *warning:* **local variable ‘max_n_mutations’ assigned but may not be used**
```r
  max_n_mutations <- n_taxa * n_nucleotides
  ^~~~~~~~~~~~~~~
```
[R/create_alignment.R:31:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment.R#L31) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/create_alignment.R:68:9:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment.R#L68) *style:* **Commented code should be removed.**
```r
    #   alignment_params = alignment_params
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:99:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment.R#L99) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:116:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment.R#L116) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_twin_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:145:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment.R#L145) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:168:69:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment.R#L168) *style:* **Commas should always have a space after.**
```r
      "Actual 'class(alignment_phydat)': ", class(alignment_phydat)," \n",
                                                                    ^
```
[R/create_alignment.R:169:55:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_alignment.R#L169) *style:* **Commas should always have a space after.**
```r
      "Actual 'alignment_phydat': ", alignment_phydat," \n"
                                                      ^
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/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/bdddec10668953ea8c65decfe0863a95c878b3e7/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/bdddec10668953ea8c65decfe0863a95c878b3e7/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/bdddec10668953ea8c65decfe0863a95c878b3e7/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/create_twin_alignment_with_standard_site_model.R:14:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_twin_alignment_with_standard_site_model.R#L14) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/create_twin_alignment_with_standard_site_model.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/create_twin_alignment_with_standard_site_model.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_twin_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/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_n_taxa.R:14:5:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_alignment_n_taxa.R#L14) *style:* **Commented code should be removed.**
```r
  # length(labels(alignment))
    ^~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_alignment_sequences.R:5:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_alignment_sequences.R#L5) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/get_default_sim_true_alignment_function.R:3:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_default_sim_true_alignment_function.R#L3) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_default_sim_true_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_default_sim_twin_alignment_function.R:4:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_default_sim_twin_alignment_function.R#L4) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_default_sim_twin_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_pir_params_filenames.R:6:17:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/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:15:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L15) *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_standard_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_sim_true_alignment_with_standard_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L12) *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:2:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L2) *warning:* **no visible binding for global variable ‘sim_twin_alignment_with_same_n_mutation’**
```r
  sim_twin_alignment_with_same_n_mutation
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L28) *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_standard_site_model_function.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_sim_twin_alignment_with_standard_site_model_function.R#L2) *warning:* **no visible binding for global variable ‘create_twin_alignment_with_standard_site_model’**
```r
  create_twin_alignment_with_standard_site_model
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_standard_site_model_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/get_sim_twin_alignment_with_standard_site_model_function.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_standard_site_model_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_run_true_tree.R:8:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/pir_run_true_tree.R#L8) *warning:* **no visible global function definition for ‘check_init_pir_params’**
```r
  check_init_pir_params(pir_params)
  ^~~~~~~~~~~~~~~~~~~~~
```
[R/pir_run.R:24:17:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/pir_run.R#L24) *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/bdddec10668953ea8c65decfe0863a95c878b3e7/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/bdddec10668953ea8c65decfe0863a95c878b3e7/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/bdddec10668953ea8c65decfe0863a95c878b3e7/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_true_alignment_with_linked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/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_linked_node_sub_site_model.R:39:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/sim_true_alignment_with_linked_node_sub_site_model.R#L39) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/sim_true_alignment_with_standard_site_model.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:27:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/sim_true_alignment_with_standard_site_model.R#L27) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/sim_true_alignment_with_unlinked_node_sub_site_model.R#L12) *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_true_alignment.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/sim_true_alignment.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:4:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L4) *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:15:3:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/sim_twin_alignment_with_same_n_mutation.R#L15) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/R/sim_twin_alignment_with_same_n_mutation.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_experiments.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_experiments.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
  cand_experiment_1$inference_model$mcmc <- cand_experiment_2$inference_model$mcmc
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:77:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_true_alignment_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(true_phylogeny = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:79:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_true_alignment_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(true_phylogeny = "irrelevant") { }
                                                                              ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_true_alignment_function.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:75:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_true_alignment_function.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:77:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_true_alignment_function.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:9:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_true_alignment_function.R#L37) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:25:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_true_alignment_function.R#L37) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:39:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_true_alignment_function.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_alignment_function.R:21:62:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:21:64:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:27:62:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L27) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:27:64:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L27) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:9:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "irrelevant" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:24:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "irrelevant" }
                       ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:45:9:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L45) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:45:25:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L45) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:47:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_alignment_function.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:66:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(one_too, many_arguments) { }
                                                                 ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:68:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(one_too, many_arguments) { }
                                                                   ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Lines should not be more than 80 characters.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:74:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
                                                                         ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:28:90:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(invalid_argument = "irrelevant") { ape::rcoal(3) }
                                                                                ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_tree_function' must be a function with one argument called 'true_phylogeny'"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Lines should not be more than 80 characters.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:72:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                       ^
```
[tests/testthat/test-check_sim_twin_tree_function.R:35:88:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                                ^
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-create_error_measure_params.R#L29) *style:* **Lines should not be more than 80 characters.**
```r
      list.files(dirname(experiment$errors_filename), pattern = basename(experiment$errors_filename))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_twin_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-create_twin_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:115:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-get_alignment_n_taxa.R#L115) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:116:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-get_alignment_n_taxa.R#L116) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_experiments_filenames.R:10:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-get_experiments_filenames.R#L10) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-get_experiments_filenames.R:32:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-get_experiments_filenames.R#L32) *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:14:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-get_pir_params_filenames.R#L14) *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:41:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-get_pir_params_filenames.R#L41) *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:65:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-get_pir_params_filenames.R#L65) *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:107:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-get_pir_params_filenames.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-pir_run.R:125:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-pir_run.R#L125) *style:* **Lines should not be more than 80 characters.**
```r
  twin_alignment <- readLines(pir_params$twinning_params$twin_alignment_filename)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_alignment_with_n_mutations.R:86:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-sim_alignment_with_n_mutations.R#L86) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-sim_true_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment.R:33:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-sim_true_alignment.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
    sim_true_alignment_function = get_sim_true_alignment_with_linked_node_sub_site_model_function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_true_alignment.R:66:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-sim_true_alignment.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    sim_true_alignment_function = get_sim_true_alignment_with_unlinked_node_sub_site_model_function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_true_alignment.R:95:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-sim_true_alignment.R#L95) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R:19:1:](https://github.com/richelbilderbeek/pirouette/blob/bdddec10668953ea8c65decfe0863a95c878b3e7/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Is it a problem that we don't generate the models for unit tests? I think it's ok, but I wanted to make sure :)


Successfully deployed to following URLs:

* https://weather-app-7zxfpw8l1.now.sh
* https://weather-app-perfect-dusky-dolphin.now.sh
* https://weather-app.ilyalesik.now.sh
* https://weather-app-git-master.ilyalesik.now.sh


That's a great catch @irshadpc! Used the file from `SE-0263` as template and somehow forgot to update some parts 🤦♂


Hi! This is the friendly automated conda-forge-webservice.

I updated the Github team because of this commit.

- @fperez was added to conda-forge. Welcome to conda-forge!
  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

You should get push access to this feedstock and CI services.

Feel free to join the community [chat room](https://gitter.im/conda-forge/conda-forge.github.io).

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
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Change video name because it was Korean naming


yes, long size is 64 bit in java and it does not depends on JVM bitness


均采用递归方式：返回在树中与val值相等的结点。  查询在树中是否存在指定结点。查询一个树是否是这个树的子树。


Nice to learn your team's research, and some suggestions are like following. Could you please send your code with the description file together? For this we learner can understand clearly, like in the ".csv" and the source code what do the code 0 and 1 stand for, 0 for shale 1 for sand, or 0 for sand 1 for shale? It will be perfect if you share the description file for the source code and the data, I think. I want to join your team togeter!


oh i was wrong


Successfully deployed to following URLs:

* https://github-api-c97zjtidp.now.sh
* https://github-api-drab-paste.now.sh
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* https://github-api-git-master.clydebts.now.sh


Is this actually intended to be `--tag foo,tag bar`, or should it rather be `--tag foo,bar`?


Regarding the commit message: This commit doesn't just update `apple.html`, before this commit it didn't even exist, please include some more information in your commit messages


Successfully deployed to following URLs:

* https://sevesosite-cegeuof5g.now.sh
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* https://sevesosite-git-master.efattal.now.sh


Successfully deployed to following URLs:

* https://tietokoneen-toiminnan-jatkokurssi-material-6dwr8jcyd.now.sh
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* https://tietokoneen-toiminnan-jatkokurssi-material.mooc.now.sh
* https://tietokoneen-toiminnan-jatkokurssi-material-git-master.mooc.now.sh


Ummm.... maybe emit paused clock must first do when action of paused in client page


I think this line is redundant