[R/alignment_params_to_posterior_trees.R:78:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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_true_alignment_function.R:27:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/R/check_sim_true_alignment_function.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
      "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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_with_n_mutations.R:36:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/R/create_alignment_with_n_mutations.R#L36) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_n_mutations <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:12:3:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/R/create_alignment.R#L169) *style:* **Commas should always have a space after.**
```r
      "Actual 'alignment_phydat': ", alignment_phydat," \n"
                                                      ^
```
[R/create_alignment.R:183:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/R/create_alignment.R#L183) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:208:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/R/create_alignment.R#L208) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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_twin_alignment_with_same_n_mutation_function.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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_standard_site_model.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/R/sim_true_alignment.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:15:3:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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:21:71:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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(one_too, many_arguments) { }
                                                                      ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:73:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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(one_too, many_arguments) { }
                                                                        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:75:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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:30:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/tests/testthat/test-check_sim_true_alignment_function.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function with one argument called 'true_phylogeny'"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:9:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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_alignment_with_n_mutations.R:86:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/tests/testthat/test-create_alignment_with_n_mutations.R#L86) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-create_alignment.R:58:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/tests/testthat/test-create_alignment.R#L58) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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/a0d5126770b278f7ea223e18d14d521c3955c678/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_true_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/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:58:1:](https://github.com/richelbilderbeek/pirouette/blob/a0d5126770b278f7ea223e18d14d521c3955c678/tests/testthat/test-sim_true_alignment.R#L58) *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/a0d5126770b278f7ea223e18d14d521c3955c678/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```


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

I updated the Github team because of this commit.

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  Go to https://github.com/orgs/conda-forge/invitation see your invitation.

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@JuliaRegistrator register


Registration pull request created: [JuliaRegistries/General/5033](https://github.com/JuliaRegistries/General/pull/5033)

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if [Julia TagBot](https://github.com/apps/julia-tagbot) is installed, or can be done manually through the github interface, or via:
```
git tag -a v0.13.1 -m "<description of version>" aa84702e7876c12d8f79b34890990f81ecd11995
git push origin v0.13.1
```


Thank you for your attention!)
macOS Mojave 10.14.6
python 2.7
Clang 4.0.1
Cmake 3.15.4

I have met all the requirements for installation
`sudo brew update
brew install build-essential ##there is not for mac os
brew install python-dev ##there is not for mac os
brew install curl unzip tar
brew install git
brew install cmake

mkdir zalf-rpm
cd zalf-rpm

git clone https://github.com/zalf-rpm/monica.git
git clone https://github.com/zalf-rpm/monica-parameters.git
git clone https://github.com/zalf-rpm/util.git
git clone https://github.com/zalf-rpm/capnproto_schemas.git
git clone https://github.com/Microsoft/vcpkg.git
build vcpkg

cd vcpkg
./bootstrap-vcpkg.sh
build zmq lib
 ./vcpkg install zeromq
 ./vcpkg install capnproto

cd ~/zalf-rpm/monica
sh update_linux.sh
cd _cmake_linux
make`  ## <- problem here
[logerr.txt](https://github.com/zalf-rpm/monica/files/3803840/logerr.txt)
<- problem here


Correct me if I'm wrong, but isn't that a different test that what was actually done ?
I mean, it should be `if ! [ -e index.php ] && ! [ -e app/AppKernel.php ]; then` (second bracket should be negated), right ?


# 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://temp1-25wnl4nur.now.sh
* https://temp1-erect-story.now.sh
* https://temp1.bansalsushil.now.sh
* https://temp1-git-master.bansalsushil.now.sh


aa


Successfully deployed to following URLs:

* https://kauri-serverless-migration-mfdbfa2zr.now.sh
* https://dev.kauri.io
* https://kauri-serverless-migration.kauri.now.sh
* https://kauri-serverless-migration-git-master.kauri.now.sh


@altheqa @support would wish we can mark spam!


[R/alignment_params_to_posterior_trees.R:78:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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_true_alignment_function.R:27:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/R/check_sim_true_alignment_function.R#L27) *style:* **Lines should not be more than 80 characters.**
```r
      "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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_with_n_mutations.R:36:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/R/create_alignment_with_n_mutations.R#L36) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_n_mutations <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:12:3:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/R/create_alignment.R#L169) *style:* **Commas should always have a space after.**
```r
      "Actual 'alignment_phydat': ", alignment_phydat," \n"
                                                      ^
```
[R/create_alignment.R:183:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/R/create_alignment.R#L183) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:208:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/R/create_alignment.R#L208) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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_twin_alignment_with_same_n_mutation_function.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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_standard_site_model.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/R/sim_true_alignment.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:15:3:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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:21:71:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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(one_too, many_arguments) { }
                                                                      ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:73:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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(one_too, many_arguments) { }
                                                                        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:75:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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:30:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/tests/testthat/test-check_sim_true_alignment_function.R#L30) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function with one argument called 'true_phylogeny'"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:9:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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_alignment_with_n_mutations.R:86:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/tests/testthat/test-create_alignment_with_n_mutations.R#L86) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-create_alignment.R:58:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/tests/testthat/test-create_alignment.R#L58) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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/f0a51409fa40acc2050d6b868a385cf295579aaf/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_true_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/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:58:1:](https://github.com/richelbilderbeek/pirouette/blob/f0a51409fa40acc2050d6b868a385cf295579aaf/tests/testthat/test-sim_true_alignment.R#L58) *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/f0a51409fa40acc2050d6b868a385cf295579aaf/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```


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Username
    <input type="text" placeholder="Enter Username" name="uname" required>


adding user name to the github


а если длина массива изменится например на 2 - то скорее всего забудешь изменить цифру 3 на 2 - мы выйдем за границу.
Лучше если функция будет принимать еще и длину массива а не только массив


testtt


We request an install of gcc-8 and gcc-8-plugin-dev, but get version 7.4.0 from gcc --version. Seems to be wrong...
And gcc_plugins are not built, because header files are not found.


зачем если можно сделать проще?
```
void ControlBall(Ball* ball)
{
    if (GetAsyncKeyState(VK_UP))
    {
        (*ball).vx += 10;
        (*ball).vy +=15;
    }

...
}
```


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.


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):
~~~


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почему MoveBall принимает массив шаров и двигает их все?
Ведь уже есть функция MoveAllBalls которая принимает массив шаров и вызывает для каждого шара MoveBall.

Получается что MoveBall должен двигать только один шар?


можно сделать проше.
```
Ball* balls = new Ball[3];
balls[0].x = 50;
balls[0].y = 400;
...
balls[1].y = 100;
balls[1].vy = 20;
balls[1].red = 40;
...
```


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* https://news-ssr-git-master.kunukn.now.sh


# 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

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|Deployment project |
----|
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check if product categories and tags are not disabled via filter - as it was done for sku above


ведь есть уже функция MoveAllBalls?
или можно прям здесь написать итерацию по массиву
```
for(..)
    MoveBall(balls[i], dt)
```


Hello


Do I need to get rid of the previously downloaded folders?


added function for checking show/not product categories - will be usefull for users who want to hide only categories in product meta


added function for checking show/not product tags - will be usefull for users who want to hide only tags in product meta


Shivangi Singh


Check if product tags are enabled


Hi


Check if product categories are enabled


Don't


@ivankravets go for archiving this project as soon as you want.


CSharpMath has depency over CSharpMath.Analyzers  which is points into ..\CSharpMath.Analyzers\CSharpMath.Analyzers\bin\Debug\netstandard1.3\CSharpMath.Analyzers.dll


check if product tags are not disabled via filter - as it was done for sku above


Successfully deployed to following URLs:

* https://news-ssr-et8uahujy.now.sh
* https://shipping-news.tech
* https://dnews.cloud
* https://news-ssr.kunukn.now.sh
* https://news-ssr-git-master.kunukn.now.sh


Could you add some docs that describe what is `BASE` and how to use it in the descriptions? Thanks!


this fixes https://github.com/sachatrauwaen/OpenContent/issues/100 ?


Husk å oppdatere avhengige scripts når endrer navn. Build er avhengig av fetch som nå heter fetch-decorator.


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* https://pavlos-portfolio-git-master.pavlos.now.sh


That should be updated.
https://github.com/verybadcat/CSharpMath/blob/a95cf98a19aec846291fe83440d59e46e98c800f/CSharpMath/CSharpMath.csproj#L40-L41
It should be like this:
https://github.com/verybadcat/CSharpMath/blob/a95cf98a19aec846291fe83440d59e46e98c800f/CSharpMath.Rendering/CSharpMath.Rendering.csproj#L46-L49


How to interpret this result?
```
13:08:52 CMD: I2cDriver10
13:08:52 MQT: stat/sonoff-13D92F/RESULT = {"I2CDriver":"10,17"}
```


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* https://crm-def-7czr14j3k.now.sh
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* https://crm-def-git-master.aodhanolan.now.sh


Font-Size


afref


Please can you do that and make a pull request ?


why you don't think about reflection in android 9?


Hello,

in my opinion and if I've understood well the purpose of the change, it is digi2raw which needs to be fixed, not the unpacker. The simulation must produce data in the same format as the hardware.

Philippe.


Don't play with feeling really


![](https://github.trello.services/images/mini-trello-icon.png) [Leetcode Problem # 242](https://trello.com/c/lxKkvLEp/9-leetcode-problem-242)


Yeah you can. At least this new commit is a more stable version of the previous ones.
This time when I make new changes, you wont have to download a new one soon. You can wait until significant and major changes have been made.

Best Regards,
Spencer A.

From: BennyHey
Sent: Monday, November 4, 2019 12:08 PM
To: adkSpence/Project-Dorian
Cc: Spencer Apeadjei-Duodu; Author
Subject: Re: [adkSpence/Project-Dorian] Bad key exception fixed. Raw key nowsaved to database (915de7d)

Do I need to get rid of the previously downloaded folders?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub, or unsubscribe.


Simplefied*


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* https://mayapurlive-git-master.mayapur.now.sh


Тоже создайте pullRequest, пожалуйста.03.11.2019, 13:29, "Анастасия Курникова" <notifications@github.com>:@PanovaElena

—You are receiving this because you were mentioned.Reply to this email directly, view it on GitHub, or unsubscribe.
-- С уважением,Елена Панова


:white_check_mark: All Rules (1 / 1) Passed

      :crown: Good job! this pull request is aligned with your organization's best practices!

      :point_right: You can review your rules settings at smart policy management :point_left:

:point_right: click here to view a full list of the events :point_left:


Successfully deployed to following URLs:

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@grasph
yeah, in principle yes. i introduced this to be able to run on open data... 2018 simulation. otherwise i'm not seeing data...


Hello the world of programming


Something bad happened here!

`<string name="monthly_map_updates"> string name=\"lat_lon_pattern\">Lat: %1$.5f Lon: %2$.5f</string </string>`

I'm sure I translated it correctly, but the system replaced the string: https://hosted.weblate.org/translate/osmand/main/pt_BR/?checksum=1e3e3c9393aebcac#history

I wasn't the only one: https://hosted.weblate.org/translate/osmand/main/pt_BR/?checksum=33fc2a8a0b1967ed#history

The issue is easy spotted by checking the "Texts with XML systax error" in the translation front page.


This commit has been deployed to DigitalOcean Spaces for easy reviewing.

| [kubernetes-tool](https://kubernetes-tool-testing.sfo2.digitaloceanspaces.com/fe2e9cdfa6cdd5a69b0ba90ac13681b886dbec75/index.html) |
|---|


I need to hold without releasing CMD+V during a timeout, only this works.


:point_right: click here to view a full list of the events :point_left:


 mikes69n / michael
Code  Issues 0  Pull requests 0  Projects 0  Wiki  Security  Pulse  Community
 michael/ eb1f5da
Initial commit

@mikes69nmikes69n committed on GitHub 24 days ago
README.md
@@ -0,0 +1 @@
# michael
1 comment on commit eb1f5da
@mikes69n
mikes69n
commented 24 days ago
README.md

Comment on eb1f5da
Leave a comment
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He'll Shivangi Singh
Welcome to hacker club of World


Is this on purpose? Why was it commented out?


The "timestamps" are not following schema.

The format should be "[-]CCYY-MM-DDThh:mm:ss[Z|(+|-)hh:mm]", i.e. there should be a "T" separating the date and time fields, not a ":".

See http://books.xmlschemata.org/relaxng/ch19-77049.html

This also applies to the https://raw.githubusercontent.com/hdscmcu/pack/master/HDSC.pidx file.

Please fix this so I can enable schema verification again for the IAR index file.


Added GruntSMBC3.cs and GruntSMBStagerC3.cs mainly to disable compression as it would be too much effort replicating the compression algorithm in CPP. I couldn't figure out how to add these files to the web front end.

This is stable for 1 grunt, but seems to cause issues if there are multiple grunts, couldn't track down why.


wow


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Are we standardising on margin/padding bottom or top? What about left and right? Let's just pick one and stick to it?


Deployment failed with the following error:

~~~
The chosen alias "preloader.now.sh" is already in use by another account.
~~~


Btw.. i've just deleted that dependency  and everything works now. Seems like it redundent.


[R/condprob_fortran.R:148:1:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/condprob_fortran.R#L148) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
condprob_dp <- function(
^
```
[R/condprob_fortran.R:222:1:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/condprob_fortran.R#L222) *style:* **functions should have cyclomatic complexity of less than 15, this has 25.**
```r
condprob_dq <- function(
^
```
[R/mbd_checks.R:9:13:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_checks.R#L9) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  births <- brts2time_intervals_and_births(brts)$births # nolint internal function
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_integrate.R:7:1:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_integrate.R#L7) *style:* **Variable and function name style should be snake_case.**
```r
mbd_ode_FORTRAN <- function(
^~~~~~~~~~~~~~~
```
[R/mbd_integrate.R:17:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_integrate.R#L17) *style:* **Variable and function name style should be snake_case.**
```r
  N <- length(initprobs)
  ^
```
[R/mbd_loglik.R:13:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_loglik.R#L13) *warning:* **no visible global function definition for ‘check_brts’**
```r
  check_brts(brts = brts, n_0 = n_0)
  ^~~~~~~~~~
```
[R/mbd_loglik.R:14:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_loglik.R#L14) *warning:* **no visible global function definition for ‘check_cond’**
```r
  check_cond(cond = cond, tips_interval = tips_interval, n_0 = n_0)
  ^~~~~~~~~~
```
[R/mbd_loglik.R:48:11:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_loglik.R#L48) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  data <- brts2time_intervals_and_births(brts) # nolint internal function
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_main_utils.R:13:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_main_utils.R#L13) *warning:* **local variable ‘pkg_name’ assigned but may not be used**
```r
  pkg_name <- get_pkg_name() # nolint internal function
  ^~~~~~~~
```
[R/mbd_main_utils.R:13:15:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_main_utils.R#L13) *warning:* **no visible global function definition for ‘get_pkg_name’**
```r
  pkg_name <- get_pkg_name() # nolint internal function
              ^~~~~~~~~~~~
```
[R/mbd_main.R:45:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_main.R#L45) *warning:* **no visible global function definition for ‘print_info’**
```r
  print_info(brts = brts, n_0 = n_0, cond = cond, verbose = verbose) # nolint internal function
  ^~~~~~~~~~
```
[R/mbd_main.R:155:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_main.R#L155) *warning:* **no visible global function definition for ‘print_info’**
```r
  print_info(brts = brts, n_0 = n_0, cond = cond, verbose = verbose) # nolint internal function
  ^~~~~~~~~~
```
[R/mbd_ml.R:20:16:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_ml.R#L20) *warning:* **no visible global function definition for ‘get_param_names’**
```r
  par_names <- get_param_names() # nolint internal function
               ^~~~~~~~~~~~~~~
```
[R/mbd_ml.R:35:19:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_ml.R#L35) *warning:* **no visible global function definition for ‘pars_transform_back’**
```r
    optim_pars <- pars_transform_back(tr_optim_pars) # nolint internal function
                  ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_ml.R:62:20:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_ml.R#L62) *warning:* **no visible global function definition for ‘pars_transform_forward’**
```r
  tr_start_pars <- pars_transform_forward(start_pars[optim_ids]) # nolint internal function
                   ^~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_pmb.R:7:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_pmb.R#L7) *warning:* **no visible global function definition for ‘check_brts’**
```r
  check_brts(brts = brts, n_0 = n_0)
  ^~~~~~~~~~
```
[R/mbd_pmb.R:21:11:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_pmb.R#L21) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  data <- brts2time_intervals_and_births(brts) # nolint internal function
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim_utils.R:14:27:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_sim_utils.R#L14) *warning:* **no visible global function definition for ‘create_singleton_phylo’**
```r
    reconstructed_tree <- create_singleton_phylo(time_points)
                          ^~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_sim_utils.R:18:27:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_sim_utils.R#L18) *warning:* **no visible global function definition for ‘create_empty_phylo’**
```r
    reconstructed_tree <- create_empty_phylo()
                          ^~~~~~~~~~~~~~~~~~
```
[R/mbd_sim.R:10:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_sim.R#L10) *warning:* **no visible global function definition for ‘check_cond’**
```r
  check_cond(cond = cond, tips_interval = tips_interval, n_0 = n_0)
  ^~~~~~~~~~
```
[R/mbd_sim.R:11:3:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_sim.R#L11) *warning:* **no visible global function definition for ‘check_seed’**
```r
  check_seed(seed = seed)
  ^~~~~~~~~~
```
[R/mbd_sim.R:25:17:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_sim.R#L25) *warning:* **no visible global function definition for ‘initialize_l_matrix’**
```r
    l_matrix <- initialize_l_matrix(age = age, n_0 = n_0)
                ^~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:2:13:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_utils.R#L2) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
  births <- brts2time_intervals_and_births(brts)$births # nolint internal function
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/mbd_utils.R:7:15:](https://github.com/Giappo/mbd/blob/4fc74cb1d8a73eb5cbd36097da4dc846db5759e2/R/mbd_utils.R#L7) *warning:* **no visible global function definition for ‘brts2time_intervals_and_births’**
```r
    births <- brts2time_intervals_and_births(brts)$births # nolint internal function
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```


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~~~
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~~~


@Magneticdud as of 0.4.4.2 release, there is a new "Check" button next to the URL input box on the options page which grants the required permission for custom URLs.


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Doesn't matter because arrays in Java can only be a signed 32bit integer in length.


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Returning ax makes sense, patch
welcome.
Prefixing with cs makes no sense if
the alternative is to simply remove
that line (all other changes done,
were not even necessary).


OK. I don't remember do we store on files RAW or DIGIs?

Is digi2raw of recent CMSSW releases producing raw data like in the real one and with FOV increment, such that the unpacker work for old and new simulation samples ?


Este codigo esta lleno de if, deberia poder optimizarse con un proveedor de estados. Saludos cordiales.


@Rocky640 If I remember correctly, I submitted the LTC for this patch before the combo patch was merged. Also, I respect your opinion but if this will pass, I will just wait for snicolet's decision.


Will fix this


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Да, стоит


lmao what


Лучше не использовать каунтеры


array.last


Пойдет без Ё


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I might misunderstand the question. I really only tested on this: http://opendata.cern.ch/record/12303
saw that the number of digis do not match and checked what current cpu version does (10 6 x). this fix works for data/simulation that i have looked at... the rest i really do not know (like digi2raw, etc...)


It's like command ``WebSensor`` but then completely different.

The problem with I2C is that it is used in drivers, sensors, displays and energy drivers. That's why I had to make a list of al current I2C drivers before implementing the possibility to disable/enable certain drivers.

Using the Index column in document ``I2CDEVICES.md`` you are now able to control individual I2C drivers with command ``I2cDriver``.

The output you see above tells you that you only have the xsns_09 and xsns_19 sensor drivers compiled and both are enabled. Command ``I2cDriver17 0`` would disable the xsns_19 sensor. It will reply with a response like
```
MQT: stat/sonoff-13D92F/RESULT = {"I2CDriver":"10,!17"}
```
Isn't that wonderful! The exclamation marks tells you the driver is disabled.

Disabling means that the code will not execute anything from the driver code. This may also be useful for debugging specific I2C driver issues.


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лучше просто менять число дней в феврале если год високосный


According to the React principles it is. Otherwise, there will be no reference to `React` when the HTML is transpired to `React.createElement`.

Reference: [https://medium.com/@Zwenza/why-do-you-need-to-import-react-in-functional-components-7385e4329ffb](https://medium.com/@Zwenza/why-do-you-need-to-import-react-in-functional-components-7385e4329ffb)


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Это излишне. Неплохо что сделал, но излишне )


That shouldn't work. You are passing `Company`, but how are you finding what it is?
This should either be implicit (no aliases in the query) or explicit (passed as arg)


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Посмотри на методы sum и take


It is better with this way:

	if ( defined( 'ICL_LANGUAGE_CODE' ) ) {
			$lang = ICL_LANGUAGE_CODE;

		} elseif ( function_exists( 'pll_current_language' ) ) {
			$lang = pll_current_language();

		} elseif ( function_exists( 'get_bloginfo' ) ) {
			$lang = get_bloginfo( 'language' );
		} else {
			$lang = 'en';
		}


Тода итоговый день можно в одну строку найти


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i make a change on line 120 of our project.


[R/hubspot_key.R:10:29:](https://github.com/lockedata/hubspot/blob/37bcfdce02af55076f8f335ffef7d5f665d53b6c/R/hubspot_key.R#L10) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
hubspot_key_get <- function(){
                            ^~
```
[R/hubspot_key.R:36:39:](https://github.com/lockedata/hubspot/blob/37bcfdce02af55076f8f335ffef7d5f665d53b6c/R/hubspot_key.R#L36) *style:* **There should be a space between right parenthesis and an opening curly brace.**
```r
hubspot_key_set <- function(key = NULL){
                                      ^~
```