[R/alignment_params_to_posterior_trees.R:78:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/R/check_sim_true_alignment_function.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_true_alignment_function <- function(sim_true_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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:51:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/check_sim_twin_alignment_function.R#L51) *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.R:12:3:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/R/create_alignment.R#L116) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:145:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/R/create_alignment.R#L169) *style:* **Commas should always have a space after.**
```r
      "Actual 'alignment_phydat': ", alignment_phydat," \n"
                                                      ^
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/R/create_copy_twin_tree_from_true_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_copy_twin_tree_from_true_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_bd_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/create_sim_bd_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_bd_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_yule_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/create_sim_yule_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_yule_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:272:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/default_params_doc.R#L272) *style:* **Lines should not be more than 80 characters.**
```r
#'   to get a function (\link{sim_true_alignment_with_linked_node_sub_site_model})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:276:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/default_params_doc.R#L276) *style:* **Lines should not be more than 80 characters.**
```r
#'   to get a function (\link{sim_true_alignment_with_unlinked_node_sub_site_model})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/R/get_alignment_sequences.R#L5) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/get_copy_true_alignment_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/get_copy_true_alignment_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_copy_true_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_pir_params_filenames.R:6:17:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/get_pir_params_filenames.R#L6) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_linked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_standard_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/get_sim_true_alignment_with_standard_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_unlinked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_standard_site_model_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/get_sim_twin_alignment_with_standard_site_model_function.R#L30) *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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```
[R/sim_true_alignment_with_linked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_true_alignment_with_linked_node_sub_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_linked_node_sub_site_model.R:39:3:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_true_alignment_with_linked_node_sub_site_model.R#L39) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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:21:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_true_alignment_with_standard_site_model.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_true_alignment_with_unlinked_node_sub_site_model.R#L13) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment.R:16:3:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_true_alignment.R#L16) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:29:3:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_twin_alignment_with_same_n_mutation.R#L29) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(twin_alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_twin_alignment_with_same_n_mutation.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_standard_site_model.R:14:3:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_twin_alignment_with_standard_site_model.R#L14) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_standard_site_model.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_twin_alignment_with_standard_site_model.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_unlinked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/R/sim_twin_alignment_with_unlinked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_experiments.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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:56:9:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L56) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:56:11:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L56) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { }
          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:58:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:63:75:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L63) *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:63:77:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L63) *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:71:9:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L71) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) {}
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:71:10:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L71) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) {}
         ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:81:9:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L81) *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:81:25:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L81) *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:83:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_true_alignment_function.R#L83) *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:36:62:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:64:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:42:62:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_twin_alignment_function.R#L42) *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:42:64:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_twin_alignment_function.R#L42) *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:51:9:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_twin_alignment_function.R#L51) *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:51:24:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_twin_alignment_function.R#L51) *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:62:9:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_twin_alignment_function.R#L62) *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:62:25:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_twin_alignment_function.R#L62) *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:64:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_sim_twin_alignment_function.R#L64) *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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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-check_twinning_params.R:209:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-check_twinning_params.R#L209) *style:* **Lines should not be more than 80 characters.**
```r
        sim_twin_alignment_function = get_sim_twin_alignment_with_standard_site_model_function()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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:111:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-get_alignment_n_taxa.R#L111) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:112:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-get_alignment_n_taxa.R#L112) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_experiments_filenames.R:10:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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/02652fe5d587be8685b41e2050c8192954380d02/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-get_temp_errors_filename.R:7:11:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-get_temp_errors_filename.R#L7) *style:* **Commas should always have a space after.**
```r
      )[1,1]
          ^
```
[tests/testthat/test-get_temp_fasta_filename.R:7:11:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-get_temp_fasta_filename.R#L7) *style:* **Commas should always have a space after.**
```r
      )[1,1]
          ^
```
[tests/testthat/test-pir_run.R:125:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-pir_run.R#L125) *style:* **Lines should not be more than 80 characters.**
```r
  twin_alignment <- readLines(pir_params$twinning_params$twin_alignment_filename)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_alignment_with_n_mutations.R:86:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-sim_alignment_with_n_mutations.R#L86) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-sim_true_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/02652fe5d587be8685b41e2050c8192954380d02/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L20) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Added indexed to receiver1 and receiver2


## This is a markdown file

Note: to see the text file pushed from my computer to the GitHub, you have to clik on Data Raw. Thanks


а как бы хотелось не играть в игру угадай индекс - ввел индекс "написало не верно", ввел другой - снова написало  что не верно... Прям экстрасенсом работаешь :D


What you describe here is a coordinate system based on the center of the pixels (as opposed to their edges).

(But the difference would be `0.5` and not `1`. And it does not even make sense to talk about a `lower right` or `upper left` of individual pixels in that system. These terms refer to the edge-based system, or to geometrical objects in any system.)

The coordinate systems of [PAGE](https://github.com/PRImA-Research-Lab/PAGE-XML/blob/b1c1986392f11f2a86974438930a917c38d0345a/pagecontent/schema/pagecontent.xsd#L2100) and [ALTO](https://github.com/altoxml/schema/blob/4ad4d3fda0f6cadfad867192826e145a2cf9b001/v4/alto-4-1.xsd#L640) are grids over the pixel edges, oriented downwards. If Tesseract's is the same, can we close the issue?


Successfully deployed to following URLs:

* https://dev-ifdh9ozei.now.sh
* https://jackleslie.now.sh
* https://jackleslie.dev
* https://dev.jackleslie.now.sh
* https://dev-git-master.jackleslie.now.sh


Successfully deployed to following URLs:

* https://my-store-admin-etpjfhq6m.now.sh
* https://my-store-admin.nexious.now.sh
* https://my-store-admin-git-master.nexious.now.sh


The setting applies to tickets that are reopened as a result of a user responding to a closed ticket. If the agent reopens the ticket, the auto assignment is still done. @protich Do you think we should change this to also apply to when an agent changes the status back to open?


Successfully deployed to following URLs:

* https://website-ik10fo709.now.sh
* https://pedroapfilho.com
* https://website.pedroapfilho.now.sh
* https://website-git-master.pedroapfilho.now.sh


с большой буквы, переменная O_o


doesn't everything has fully_qualified_name


To use the full Dataset for crossvalidation you should have 10.2 GB of FREE RAM otherwise use a part of the initial dataset like i had do.


однострочники не пишем (обычно) - правило простое - одна строка одно действие.

Это помогает при дебаге, ну и просто наглядней - а то бывают случаи когда просто глаз пропускает условие подобное.


This breaks CentOS6 and RES6, as the package is not available there. I think we should keep the `%if 0%{?fedora}`


[오픈소스+프로젝트+제안서-김상민+오준엽+박채원2+이인구2.pptx](https://github.com/inguelee/OpenSource/files/3820113/%2B.%2B.-.%2B.%2B.2%2B.2.pptx)


Adding
plot1.R
plot1.png
plot1.R
plot2.png
plot3.R
plot3.png
plot4.R
plot4.png


"else return false;"?


Successfully deployed to following URLs:

* https://deags3000githubio-c53d8itbg.now.sh
* https://deags3000githubio.deags3000.now.sh
* https://deags3000githubio-git-master.deags3000.now.sh


чую где-то подвох - метод`storage.addCarAfterI` не отнимает index, а тут отнимается...


The first check (for BubbleColumnBlock) isn't needed anymore.


And same here,  as `perl-generators` doesn't neither exists at CentOS6 or RES6.


я посмотрела )


# 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://ffconf-next-workshop-3co4y4p26.now.sh
* https://ffconf-next-workshop.jedd.now.sh
* https://ffconf-next-workshop-git-master.jedd.now.sh


return on new line, to follow the existing coding style.


еще один год проверяет по совпадению в строке. Ну ведь это слегка не интуитивно :)
Да я сказал что так делать, но есть люди кто так не сделал, и тут они правы. Правда идеальное решение никто досихпор не написал, ладно вдруг найду.


@aydreeihn - Yes, we should apply same on agent's action.


wrapped the expensive write op in an if so that its cheaper for even splits


Successfully deployed to following URLs:

* https://kth-courses-huzh0g9vh.now.sh
* https://kth-courses.tko.now.sh
* https://kth-courses-git-master.tko.now.sh


Will you send a PR @nvlsianpu?


Ah okay, thanks for explaining


Fair point, I just copy pasted it from the previous migration. I'll change it to 2019,10,1!


Should not the tx.vin[i].scriptWitness.stack.back().size() be checked too?


Successfully deployed to following URLs:

* https://create-tinder-1utrej5tl.now.sh
* https://create-tinder.seamusreeve.now.sh
* https://create-tinder-git-master.seamusreeve.now.sh


ух... опасно. Будь это реальный код не пропустили. Да в твоем случае зная что делает хранилище этот код на самом деле рабочий. Но давай на секунду представим что хранилище удаляет данные не сразуже, а спустя некоторое время. что будет?


good stuff bro


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

I updated the Github team because of this commit.

- @jorisvandenbossche was added to this feedstock maintenance team.

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

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

NOTE: Please make sure to not push to the repository directly.
      Use branches in your fork for any changes and send a PR.
      More details [here](https://conda-forge.org/docs/maintainer/updating_pkgs.html#forking-and-pull-requests)


[![Visit Site](https://raw.githubusercontent.com/pantheon-systems/ci-drops-8/0.1.0/data/img/visit-site-36.png)](https://pr-65-reits-across-america-d8.pantheonsite.io/)

Created multidev environment [pr-65](https://dashboard.pantheon.io/sites/afa5510e-3253-42b8-b3a4-35622f7e9eae#pr-65) for reits-across-america-d8.


ADD  NEW HTML document


Successfully deployed to following URLs:

* https://code2go-hwos6nupn.now.sh
* https://code2go.dev
* https://code2go.medienwerk.now.sh
* https://code2go-git-master.medienwerk.now.sh


`finalInt <= 0`
и да скобок на этой строке что-то многовато для swift


если просто удалить else тут и предыдущий, то можно будет написать одну строчку `return finalInt` и все останется рабочим.

P.S. ну и вложенные условия заодно уйдут.


Successfully deployed to following URLs:

* https://relational-playground-k6u9uxa5n.now.sh
* https://relationalplayground.com
* https://relational-playground.michaelmior.now.sh
* https://relational-playground-git-master.michaelmior.now.sh


а тут еще и побочный эффект - она не только проверяет, но и меняет состояние интерфейса (консоли)


Successfully deployed to following URLs:

* https://rc-field-form-nsvt2ijen.now.sh
* https://rc-field-form.react-component.now.sh
* https://rc-field-form-git-master.react-component.now.sh


как бы хотелось относительный путь...


Usando métodos


Lib is not needed anymore. Remove?


обращаю внимание как названа функция которую вызываешь, и как твоя - есть разница?


this is fine, but you could also just `.toOption` an either if you import `cats.syntax.either._`


снова с большой буквы переменная


Successfully deployed to following URLs:

* https://eloc-1g6jbmolm.now.sh
* https://eloc.now.sh
* https://eloc.amio1.now.sh
* https://eloc-git-master.amio1.now.sh


Successfully deployed to following URLs:

* https://deags3000githubio-k833qfovc.now.sh
* https://deags3000githubio.deags3000.now.sh
* https://deags3000githubio-git-master.deags3000.now.sh


![InkedScreenshot_20191106-011311_Settings_LI](https://user-images.githubusercontent.com/55696282/68398588-56cb5d80-01b8-11ea-8cb6-9c8321b842f9.jpg)
라즈베리파이이름을 HighVoltages로 바꾸고나서 연결을 할려고했다.


# 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)|


You'ld rather merge the `{{ kernel }}` and `{{ boot.kernel }}`


Ha, is that what it was in the end?!? Gah!


changed to use `toOption`


что за желание запихнуть save в load? :D ну это же не логично.


Successfully deployed to following URLs:

* https://deags3000githubio-ihfi7rnq5.now.sh
* https://deags3000githubio.deags3000.now.sh
* https://deags3000githubio-git-master.deags3000.now.sh


I reverted the entire PR from Matt because it turned out he hadn't tested it, but written the code to what he assumed was correct, according to the datasheet, and then posted the PR. It turned out the code was wrong, but his idea that this section should be redone was very correct ;)

I just fixed it and made the whole RSSI business more obvious. The RSSI and SNR code now also includes the slope correction and low SNR corrections mentioned in the datasheet. It's pushed to the repo now, and tagged as release v1.11. The precompiled firmware is also updated.

The RSSI value is still sent as a unsigned 8-bit integer, so whatever host reads it should just subtract 157 to get the actual RSSI. This is updated in the library as well.


Successfully deployed to following URLs:

* https://ffconf-next-workshop-b2y93t4oh.now.sh
* https://ffconf-next-workshop.jedd.now.sh
* https://ffconf-next-workshop-git-master.jedd.now.sh


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 770-IDAM-248-Sign-Out-Te](https://teamcity.nice.org.uk/viewLog.html?buildId=61260&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **SUCCESS**
Summary: Running Build time: 00:05:40


Could we link to https://github.com/multiformats/multicodec instead? I think for such things the more central the better.


Successfully deployed to following URLs:

* https://dancernotes-graphql-rfqeapyp6.now.sh
* https://dancernotes-graphql.cghayden.now.sh
* https://dancernotes-graphql-git-master.cghayden.now.sh


    :x: Test Failed: va/tests/accessibility

composer va:test:accessibility

```
audited 183 packages in 1.591s
found 2 low severity vulnerabilities
  run `npm audit fix` to fix them, or `npm audit` for details

> axe_tests@1.0.0 test /var/aegir/projects/cms/pr680
> node ./tests/accessibility/aXeAccessibilityCheck.js

!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov 0
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/sections  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/landing_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/documentation_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/event  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/health_care_local_facility  = 1
[ { id: 'label',
    impact: 'critical',
    tags:
     [ 'cat.forms',
       'wcag2a',
       'wcag332',
       'wcag131',
       'section508',
       'section508.22.n' ],
    description: 'Ensures every form element has a label',
    help: 'Form elements must have labels',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/label?application=webdriverjs',
    nodes:
     [ [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object],
       [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/health_care_region_detail_page  = 1
[ { id: 'duplicate-id',
    impact: 'minor',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description: 'Ensures every id attribute value is unique',
    help: 'id attribute value must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id?application=webdriverjs',
    nodes: [ [Object], [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/health_care_region_page  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/office  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/outreach_asset  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/person_profile  = 1
[ { id: 'duplicate-id-aria',
    impact: 'critical',
    tags: [ 'cat.parsing', 'wcag2a', 'wcag411' ],
    description:
     'Ensures every id attribute value used in ARIA and in labels is unique',
    help: 'IDs used in ARIA and labels must be unique',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/duplicate-id-aria?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/press_release  = 1
[ { id: 'aria-allowed-attr',
    impact: 'critical',
    tags: [ 'cat.aria', 'wcag2a', 'wcag412' ],
    description: 'Ensures ARIA attributes are allowed for an element\'s role',
    help: 'Elements must only use allowed ARIA attributes',
    helpUrl:
     'https://dequeuniversity.com/rules/axe/3.3/aria-allowed-attr?application=webdriverjs',
    nodes: [ [Object] ] } ]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/regional_health_care_service_des  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/news_story  = 0
[]
!!!  NUMBER OF NEW VIOLATIONS on http://pr680.ci.cms.va.gov/node/add/support_service  = 0
[]
!!!  VIOLATION TYPES FOUND: 5 PROCESS EXITED WITH CODE 1  !!!
> npm install --only=production
> npm test
Thu, 07 Nov 2019 14:46:02 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:44:14
Thu, 07 Nov 2019 14:46:05 GMT axe-webdriverjs deprecated Error must be handled as the first argument of axe.analyze. See: #83 at tests/accessibility/aXeAccessibilityCheck.js:56:42
Failed to inject axe-core into one of the iframes!
Failed to inject axe-core into one of the iframes!
npm ERR! Test failed.  See above for more details.
Script npm test handling the va:test:accessibility event returned with error code 1
```

- **On:** devshop.cms.va.gov
- **In:** 01:14


It was 4.6 actually, not 4.16.


ye waaala dala. aisehi..


Successfully deployed to following URLs:

* https://deags3000githubio-37bdfegzc.now.sh
* https://deags3000githubio.deags3000.now.sh
* https://deags3000githubio-git-master.deags3000.now.sh


![20191106_011422품질저하](https://user-images.githubusercontent.com/55696282/68399009-0f919c80-01b9-11ea-9754-ee81cce1dc80.jpg)
블루투스를 연결 되었지만


Successfully deployed to following URLs:

* https://eloc-cfq8oq2tk.now.sh
* https://eloc.now.sh
* https://eloc.amio1.now.sh
* https://eloc-git-master.amio1.now.sh


![20191106_011442품질저하](https://user-images.githubusercontent.com/55696282/68399142-48317600-01b9-11ea-853d-d01d6d9c392e.jpg)
연결이 실패한다는 메시지가 뜬다.

 그래서 양쪽 USB선을 사서 서로라즈베리파이연결되는지 해봤지만 연결이 안되서 미팅을 마무리가 되었다.


You can't do that, you're using the variable before it is defined (ESlint warns about it so please read those messages as they will hint you about errors in your code).
<img width="828" alt="bild" src="https://user-images.githubusercontent.com/110222/68399177-485c5200-0176-11ea-8011-559b3f5d71b2.png">


Uploaded test apks for
 - [**armv7**](https://download.opengis.ch/qfield/ci-builds/qfield-dev--cb5396cb814371c0713b97c636dbbaf3b52d1d87-armv7.apk)
 - [arm64_v8a](https://download.opengis.ch/qfield/ci-builds/qfield-dev--cb5396cb814371c0713b97c636dbbaf3b52d1d87-arm64_v8a.apk)
 - [x86](https://download.opengis.ch/qfield/ci-builds/qfield-dev--cb5396cb814371c0713b97c636dbbaf3b52d1d87-x86.apk)
 - [x86_64](https://download.opengis.ch/qfield/ci-builds/qfield-dev--cb5396cb814371c0713b97c636dbbaf3b52d1d87-x86_64.apk)


teste


Thanks for the reminder, I'll get the tag pushed up soon.


[R/alignment_params_to_posterior_trees.R:78:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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_inference_conditions.R:17:3:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/check_inference_conditions.R#L17) *warning:* **no visible global function definition for ‘check_model_type’**
```r
  check_model_type(inference_conditions$model_type)
  ^~~~~~~~~~~~~~~~
```
[R/check_init_pir_params.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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_model_type.R:4:18:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/check_model_type.R#L4) *warning:* **no visible global function definition for ‘get_model_types’**
```r
  model_types <- get_model_types()
                 ^~~~~~~~~~~~~~~
```
[R/check_pir_out.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/R/check_sim_true_alignment_function.R#L9) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_true_alignment_function <- function(sim_true_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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:51:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/check_sim_twin_alignment_function.R#L51) *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.R:12:3:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/R/create_alignment.R#L116) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:145:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/R/create_alignment.R#L169) *style:* **Commas should always have a space after.**
```r
      "Actual 'alignment_phydat': ", alignment_phydat," \n"
                                                      ^
```
[R/create_all_experiments.R:24:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/R/create_copy_twin_tree_from_true_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_copy_twin_tree_from_true_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_bd_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/create_sim_bd_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_bd_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_sim_yule_twin_tree_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/create_sim_yule_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_yule_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:272:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/default_params_doc.R#L272) *style:* **Lines should not be more than 80 characters.**
```r
#'   to get a function (\link{sim_true_alignment_with_linked_node_sub_site_model})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/default_params_doc.R:276:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/default_params_doc.R#L276) *style:* **Lines should not be more than 80 characters.**
```r
#'   to get a function (\link{sim_true_alignment_with_unlinked_node_sub_site_model})
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/R/get_alignment_sequences.R#L5) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/get_copy_true_alignment_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/get_copy_true_alignment_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_copy_true_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_pir_params_filenames.R:6:17:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/get_pir_params_filenames.R#L6) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_linked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_standard_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/get_sim_true_alignment_with_standard_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L20) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_unlinked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L29) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_standard_site_model_function.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/get_sim_twin_alignment_with_standard_site_model_function.R#L30) *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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/R/select_candidate_evidences.R#L25) *style:* **functions should have cyclomatic complexity of less than 15, this has 20.**
```r
select_candidate_evidences <- function(
^
```
[R/sim_true_alignment_with_linked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_true_alignment_with_linked_node_sub_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_linked_node_sub_site_model.R:39:3:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_true_alignment_with_linked_node_sub_site_model.R#L39) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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:21:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_true_alignment_with_standard_site_model.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_true_alignment_with_unlinked_node_sub_site_model.R#L13) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment.R:16:3:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_true_alignment.R#L16) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:29:3:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_twin_alignment_with_same_n_mutation.R#L29) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(twin_alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_twin_alignment_with_same_n_mutation.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_standard_site_model.R:14:3:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_twin_alignment_with_standard_site_model.R#L14) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_standard_site_model.R:30:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_twin_alignment_with_standard_site_model.R#L30) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_unlinked_node_sub_site_model.R:11:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/R/sim_twin_alignment_with_unlinked_node_sub_site_model.R#L11) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_experiments.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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:56:9:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L56) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:56:11:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L56) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { }
          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:58:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L58) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:63:75:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L63) *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:63:77:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L63) *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:71:9:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L71) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) {}
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:71:10:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L71) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) {}
         ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:81:9:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L81) *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:81:25:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L81) *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:83:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_true_alignment_function.R#L83) *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:36:62:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:64:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:42:62:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_twin_alignment_function.R#L42) *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:42:64:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_twin_alignment_function.R#L42) *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:51:9:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_twin_alignment_function.R#L51) *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:51:24:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_twin_alignment_function.R#L51) *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:62:9:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_twin_alignment_function.R#L62) *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:62:25:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_twin_alignment_function.R#L62) *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:64:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_sim_twin_alignment_function.R#L64) *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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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-check_twinning_params.R:209:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-check_twinning_params.R#L209) *style:* **Lines should not be more than 80 characters.**
```r
        sim_twin_alignment_function = get_sim_twin_alignment_with_standard_site_model_function()
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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:111:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-get_alignment_n_taxa.R#L111) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:112:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-get_alignment_n_taxa.R#L112) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_experiments_filenames.R:10:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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/b14819ce84250f88e80374be4252165deb12144c/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-get_temp_errors_filename.R:7:11:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-get_temp_errors_filename.R#L7) *style:* **Commas should always have a space after.**
```r
      )[1,1]
          ^
```
[tests/testthat/test-get_temp_fasta_filename.R:7:11:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-get_temp_fasta_filename.R#L7) *style:* **Commas should always have a space after.**
```r
      )[1,1]
          ^
```
[tests/testthat/test-pir_run.R:125:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-pir_run.R#L125) *style:* **Lines should not be more than 80 characters.**
```r
  twin_alignment <- readLines(pir_params$twinning_params$twin_alignment_filename)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_alignment_with_n_mutations.R:86:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-sim_alignment_with_n_mutations.R#L86) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment_with_standard_site_model.R:17:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-sim_true_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/b14819ce84250f88e80374be4252165deb12144c/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L20) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Successfully deployed to following URLs:

* https://next-ts-boilerplate-j6gi3wg22.now.sh
* https://next-ts-boilerplate.vararu.org
* https://next-ts-boilerplate.tvararu.now.sh
* https://next-ts-boilerplate-git-master.tvararu.now.sh


Successfully deployed to following URLs:

* https://musicvararuorg-bh0wc4vmx.now.sh
* https://music.vararu.org
* https://musicvararuorg.tvararu.now.sh
* https://musicvararuorg-git-master.tvararu.now.sh


I filed [JDK-8233798](https://bugs.openjdk.java.net/browse/JDK-8233798) to track this.


Successfully deployed to following URLs:

* https://free-fitness-orohusvf7.now.sh
* https://free-fitness.by
* https://free-fitness.happylolonly.now.sh
* https://free-fitness-git-develop.happylolonly.now.sh


Successfully deployed to following URLs:

* https://terrierdev-6g0ax73ft.now.sh
* https://now.terrier.dev
* https://www.terrier.dev
* https://terrier.now.sh
* https://terrierdev.terrierscript.now.sh
* https://terrierdev-git-master.terrierscript.now.sh


TeamCity Identity and Access Management / Identity - ManagementPortal [Build 771-r6E51BAE](https://teamcity.nice.org.uk/viewLog.html?buildId=61263&buildTypeId=IdentityandAccessManagement_BuildRoleManagementPortal) outcome was **SUCCESS**
Summary: Running Build time: 00:04:07


Successfully deployed to following URLs:

* https://khromedev-46hc9j5wr.now.sh
* https://khrome.dev
* https://khromedev.khrome83.now.sh
* https://khromedev-git-master.khrome83.now.sh


In addition, the kind of check you're doing is useless: either we supply a value so array deconstruction will read a value, or we don't (in that case the value will be `undefined` and the supplied default will be used). I can't see why you're doing this really.


Successfully deployed to following URLs:

* https://ffconf-next-workshop-eqnjlbc97.now.sh
* https://ffconf-next-workshop.jedd.now.sh
* https://ffconf-next-workshop-git-master.jedd.now.sh


This is part of the original theme. Maybe I misunderstand why this folder wasn't copied in the initial commit? Without it the theme is broken on my machine.


@elpiankova оно у меня в переменной "с" в принте она перед длиной строки


@elpiankova


Successfully deployed to following URLs:

* https://eloc-enokffub3.now.sh
* https://eloc.now.sh
* https://eloc.amio1.now.sh
* https://eloc-git-master.amio1.now.sh


use the `context['boot']['kernel']` that you just created


Left a few comments, but looks rather good!


This check is not necessary.


col Area또한 전체파트만 해준거임.


我就想修改一下


thanks, must have been autogenerated when the module was added


In Django templates there is a better way to write a message if a loop is empty. It is built-in.


Successfully deployed to following URLs:

* https://copperconnector-jsv28ibwq.now.sh
* https://copperconnector.now.sh
* https://copperconnector.modelb.now.sh
* https://copperconnector-git-master.modelb.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

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)|


<details>

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

Taskcluster-GitHub attempted to create a task for this event with the following scopes:

```
[
  "assume:repo:github.com/mozilla/bugbug:branch:master",
  "queue:route:statuses",
  "queue:scheduler-id:taskcluster-github"
]
```

The expansion of these scopes is not sufficient to create the task, leading to the following:

Client ID static/taskcluster/github does not have sufficient scopes and is missing the following scopes:

```
{
  "AnyOf": [
    {
      "AnyOf": [
        "queue:create-task:highest:aws-provisioner-v1/github-worker",
        "queue:create-task:very-high:aws-provisioner-v1/github-worker",
        "queue:create-task:high:aws-provisioner-v1/github-worker",
        "queue:create-task:medium:aws-provisioner-v1/github-worker",
        "queue:create-task:low:aws-provisioner-v1/github-worker",
        "queue:create-task:very-low:aws-provisioner-v1/github-worker",
        "queue:create-task:lowest:aws-provisioner-v1/github-worker"
      ]
    },
    {
      "AnyOf": [
        "queue:create-task:aws-provisioner-v1/github-worker",
        {
          "AllOf": [
            "queue:define-task:aws-provisioner-v1/github-worker",
            "queue:task-group-id:taskcluster-github/cyOoa3NjT_-l6v6qUIWY3A",
            "queue:schedule-task:taskcluster-github/cyOoa3NjT_-l6v6qUIWY3A/E5pXP-quR3ipD17qsg8g_A"
          ]
        }
      ]
    }
  ]
}
```

This request requires the client to satisfy the following scope expression:

```
{
  "AllOf": [
    "queue:route:statuses",
    {
      "AnyOf": [
        {
          "AllOf": [
            "queue:scheduler-id:taskcluster-github",
            {
              "AnyOf": [
                "queue:create-task:highest:aws-provisioner-v1/github-worker",
                "queue:create-task:very-high:aws-provisioner-v1/github-worker",
                "queue:create-task:high:aws-provisioner-v1/github-worker",
                "queue:create-task:medium:aws-provisioner-v1/github-worker",
                "queue:create-task:low:aws-provisioner-v1/github-worker",
                "queue:create-task:very-low:aws-provisioner-v1/github-worker",
                "queue:create-task:lowest:aws-provisioner-v1/github-worker"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:aws-provisioner-v1/github-worker",
            {
              "AllOf": [
                "queue:define-task:aws-provisioner-v1/github-worker",
                "queue:task-group-id:taskcluster-github/cyOoa3NjT_-l6v6qUIWY3A",
                "queue:schedule-task:taskcluster-github/cyOoa3NjT_-l6v6qUIWY3A/E5pXP-quR3ipD17qsg8g_A"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-11-07T14:59:05.290Z

</details>


Successfully deployed to following URLs:

* https://copperconnector-2bo9ybw6g.now.sh
* https://copperconnector.now.sh
* https://copperconnector.modelb.now.sh
* https://copperconnector-git-master.modelb.now.sh


Yes, that's a good solution. I'll write it as bst_mat2py. Sorry, I hadn't seen bst_py2mat yet, still slowly going through the code. Thanks!


Hi, I am a MSc student in Computer Science and I need to submit an article with the theme: SACK Panic, but I did not find any article or tutorial on how to simulate this attack using a virtual machine, in this work I need to simulate this SACK attack on VirtualBOX, can anyone help? Thanks.


Successfully deployed to following URLs:

* https://terrierdev-3r9ltlg90.now.sh
* https://now.terrier.dev
* https://www.terrier.dev
* https://terrier.now.sh
* https://terrierdev.terrierscript.now.sh
* https://terrierdev-git-master.terrierscript.now.sh


The reason behind this was to set a default value in case the variables wasn't defined in the `config`, i.e. you haven't pressed _Save_ in `admin`.


Successfully deployed to following URLs:

* https://jw-6e73zfpca.now.sh
* https://jw-itchy-twist.now.sh
* https://jw.wj9.now.sh
* https://jw-git-master.wj9.now.sh