[R/alignment_params_to_posterior_trees.R:78:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/create_sim_yule_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_yule_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/get_pir_params_filenames.R#L6) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R:15:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L15) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_linked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_standard_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/get_sim_true_alignment_with_standard_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_unlinked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/sim_true_alignment_with_standard_site_model.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:27:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/sim_true_alignment_with_standard_site_model.R#L27) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:13:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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:13:3:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/sim_true_alignment.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:10:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L10) *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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_experiments.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
  cand_experiment_1$inference_model$mcmc <- cand_experiment_2$inference_model$mcmc
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:77:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_sim_true_alignment_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(true_phylogeny = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:79:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_sim_true_alignment_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(true_phylogeny = "irrelevant") { }
                                                                              ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_sim_true_alignment_function.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:75:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_sim_true_alignment_function.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:77:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_sim_true_alignment_function.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:9:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_sim_true_alignment_function.R#L37) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:25:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_sim_true_alignment_function.R#L37) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:39:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-check_sim_true_alignment_function.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:62:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-get_temp_errors_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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/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/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-sim_true_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment.R:33:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-sim_true_alignment.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
    sim_true_alignment_function = get_sim_true_alignment_with_linked_node_sub_site_model_function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_true_alignment.R:51:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-sim_true_alignment.R#L51) *style:* **Lines should not be more than 80 characters.**
```r
    sim_true_alignment_function = get_sim_true_alignment_with_unlinked_node_sub_site_model_function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R:20:1:](https://github.com/richelbilderbeek/pirouette/blob/0ef80399cb0ee73fa091189f110139c5f2fae2a5/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L20) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Wrong url for the gem


[CL的修改前调查.txt](https://github.com/RayXu14/OpenNMT-py/files/3818325/CL.txt)


Update path for product controller


## 情报
1. field在数据预处理的时候已经决定，但其中包含会影响train的功能。
    * 单单迭代器的话，仍然可以通过再包一层iterator的包装避免修改之
    * 看到数据刚出batch，tgt就有bos了，判断在预处理的时候已经加入
        * Trainer._gradient_accumulation（已pdb确认，bos id为2
3. 如果要从batch.tgt上下手，不管是从预处理还是训练入手，train和valid都需要分别注意
    * Trainer._gradient_accumulation（已pdb确认，bos id为2
    * Trainer.validate（已pdb确认，bos id为2
    * 可以预见由于translate的时候不经由预处理，所以不论哪种方式，translate都要单独修改
4. 由于fields load了下面两个地方，而且field貌似已经定型，所以这里建议还是从预处理部分改一改
    * onmt/bin/train.train
    * onmt/train_single.main

## 应对
1. 预处理阶段：添加-cross_lingual参数，若为真则为每个数据来源在decoder阶段，启用单独的tgt bos。为此要对shared的词表或者tgt词表加入每个语言独立的bos。
    * onmt/opt.preprocess_opts
    * onmt/utils/parse.ArgumentParser.validate_preprocess_args
    * onmt/bin/preprocess.build_save_dataset
        * 目前的写法是放入tgt的counter。如果二者share，必然也会进入shared的词表。
        * 唯一的疑虑是，对于bos的频率，我仅仅采用了counter里面最大的一个，同等赋值之，希望不会有问题。
2. 训练阶段：添加-cross_lingual参数。在train和valid，让batch附带数据集id进行输出，并且在batch出来的位置，带出语种对应bos的词id，准备下一步替换tensor的bos。
    * onmt/opt.preprocess_opts
    * onmt/inputters/inputter.py
    * onmt/trainer.build_trainer
    * onmt/trainer.Trainer.__init__
    * onmt/trainer.Trainer._gradient_accumulation
    * onmt/train_single.main
    * 加了cross_lingual选项理论上就已经无法复现之前的结果了。（虽然最小词频默认是0，但是貌似onmt还是会在那里筛选一下，多了两个词后，词总数居然还是不变，因此会修改词表。）因此验证没有加cross_lingual的选项是否还兼容之前的表现。
        * 验证单训daily5w
            * 不share vocab：完全一致
            * share vocab & share embeddings：完全一致
            * share vocab 不share embeddings：完全一致
        * 验证dl5w&wb50w-1vs1，不cross_lingual（注意dataset也要换成不带CLversion的版本）
            * 不share vocab：完全一致
            * share vocab & share embeddings：完全一致
            * share vocab 不share embeddings：完全一致
3. 替换输入model的 tgt tensor的bos（略）
4. 对应在translate阶段增加选项
    * onmt/opts.translate_opts
    * onmt/translate/translator
    * 确认兼容过去的（不带override_bos的）翻结果生成，结果完全一致


Update the path for the product controller test


Successfully deployed to following URLs:

* https://clem-ivghauj26.now.sh
* https://clem.jcada.now.sh
* https://clem-git-master.jcada.now.sh


This code is not related with the sequence of the book


update PHC list


🔥 Device tests completed (Failed) on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3221658)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/device-tests-yaml/1eaf885220be4ad377ca8bff224899e9520a0c3d/3221658/device-tests/jenkins-results/tests/index.html) 🔥

# Test results

<details>
<summary>8 tests failed, 105 tests passed.</summary>

## Failed tests

 * link all/iOS Unified 64-bits - device/Release: TimedOut
 * link all/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): TimedOut
 * link sdk/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): TimedOut
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): Failed
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (debug): Failed
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/Release: TimedOut
 * [NUnit] Mono BCL tests group 2/iOS Unified 64-bits - device/AssemblyBuildTarget: SDK framework (release): TimedOut
 * [xUnit] Mono BCL tests group 3/iOS Unified 64-bits - device/AssemblyBuildTarget: dylib (debug): TimedOut
</details>


Successfully deployed to following URLs:

* https://rolandoio-9caswrpqu.now.sh
* https://rolando.io
* https://rolandoio.rlx310.now.sh
* https://rolandoio-git-master.rlx310.now.sh


Commit 2a455d4 was attributed to user "root" so I don't know if anyone will be alerted to my comment there, but this LDAP server should not be included as the default authentication method.


Build version: __`0.11.0-master.1163`__ :crossed_fingers: [`master`](https://github.com/streamich/ci-scripts/tree/master) on [*CircleCI*](https://circleci.com/gh/streamich/ci-scripts/1163) :tada:


Wrong url for the gem pg_search


Successfully deployed to following URLs:

* https://portfolio-bt43ziy7y.now.sh
* https://yuwen-li.com
* https://www.yuwen-li.com
* https://portfolio.muzlee1113.now.sh
* https://portfolio-git-master.muzlee1113.now.sh


@Alexpux why was the patch dropped?


Build version: __`0.11.0-master.1800`__ :crossed_fingers: [`master`](https://github.com/streamich/ci-scripts/tree/master) on [*Travis*](https://travis-ci.org/streamich/ci-scripts/builds/608601390) :tada:


You're welcome. 😁 I'm hoping to have a new release on the weekend


Successfully deployed to following URLs:

* https://news-ssr-27y9mqas1.now.sh
* https://shipping-news.tech
* https://dnews.cloud
* https://news-ssr.kunukn.now.sh
* https://news-ssr-git-master.kunukn.now.sh


Successfully deployed to following URLs:

* https://clem-gstrhhm3f.now.sh
* https://clem.jcada.now.sh
* https://clem-git-master.jcada.now.sh


> What is a full command line to start a network game? By using `-solo-net` or `-deathmatch -warp 01` framerate is fine.

I guess you can just add it to the setup's command line? Else, there is the `-server` parameter, but then you'll have to connect a second instance to it. Not sure what exactly the setup tool does, though.


'TV' must be in lower case for test if the filter work with up or down case


Successfully deployed to following URLs:

* https://react-hook-form-website-851zmmt7m.now.sh
* https://react-hook-form.com
* https://www.react-hook-form.com
* https://react-hook-form-website.bluebill1049.now.sh
* https://react-hook-form-website-git-master.bluebill1049.now.sh


Successfully deployed to following URLs:

* https://clem-91ucza0gh.now.sh
* https://clem.jcada.now.sh
* https://clem-git-master.jcada.now.sh


Successfully deployed to following URLs:

* https://kybervirtualhackathon-6661gde95.now.sh
* https://defizap.com
* https://kybervirtualhackathon.botforkybergang.now.sh
* https://kybervirtualhackathon-git-master.botforkybergang.now.sh


That's really an impressive effect! I'll see if I can emulate it with the paletted renderer - just for fun. It will of course look even more impressive with the truecolor renderer.


Successfully deployed to following URLs:

* https://clem-knsjity3q.now.sh
* https://clem.jcada.now.sh
* https://clem-git-master.jcada.now.sh


The scope 'recent' doesn't receive a parameter an .present? is redundant


Successfully deployed to following URLs:

* https://clem-jl3r5wtzg.now.sh
* https://clem.jcada.now.sh
* https://clem-git-master.jcada.now.sh


Btw - centering was not corrupted by Nautilus7 but by @littlesat in skin.py + skin.xml. I think, due EPGImport plugin and changes in Directories. There was used smaller picture before, but after changes in Directories it is not possible more and is used bigger png.


esqueci aqui de retornar false no else


review


Successfully deployed to following URLs:

* https://clem-okgps8s24.now.sh
* https://clem.jcada.now.sh
* https://clem-git-master.jcada.now.sh


operador ternário, preciso me aprimorar e usar essencialmente (sempre que possível) usar ele


why?


What is broken exactly?

czw., 7 lis 2019, 06:49 użytkownik NICHOLAS85 <notifications@github.com>
napisał:

> Did you mean to place this after shift $?, my config seems to have broken
> after this commit.
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/zdharma/zplugin/commit/8392547590b8b0a05b67db35447750d3706ffe71?email_source=notifications&email_token=ABOE4CHMWOSYLLOB2OC53W3QSOT6PA5CNFSM4JKBZHH2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBCF2HA#commitcomment-35842272>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ABOE4CGW75X7L3I243AYNNTQSOT6PANCNFSM4JKBZHHQ>
> .
>


Successfully deployed to following URLs:

* https://rymatecouk-gbj980bwo.now.sh
* https://rymate-dev.now.sh
* https://rymatecouk.ryanmurthick.now.sh
* https://rymatecouk-git-master.ryanmurthick.now.sh


Is this really part of 1.12.0...?


Thanks!


Successfully deployed to following URLs:

* https://rymatecouk-jlcb2iv53.now.sh
* https://rymate-dev.now.sh
* https://rymatecouk.ryanmurthick.now.sh
* https://rymatecouk-git-master.ryanmurthick.now.sh


alterei um pouquinho as 'nomenclaturas' para os níveis xD


네트워크(여러 사람과 채팅), Master Detail 추가 설명(1:N의 관계)

1:1이 아닌 여러 사람이 접속 가능하게

실무에서 사용할 네트워크 클래스 -> URLReaderV1.class
--> 서버어플리케이션 할 때 개념이 헷갈림(URI,URL)
URL : 네이버/index.html(대문)
URI : /news/~~~~~~~~~,,,,,,,,,Path라고 부르는 com 다음 첫번째 /
	여기서는 news

--------
데이터 가져오는 가장 기본적인 코드
URLConnectionReader 클래스에

------------------------------------------------------
oracle
***********Master Detail 추가 설명,, 1:N, 1 대 다의 관계


✅ Device tests passed on iOS on [Azure DevOps](https://dev.azure.com/devdiv/DevDiv/_build/index?buildId=3221880)(iOS): [Html Report](http://xamarin-storage/jenkins/xamarin-macios/d16-4/011aaf7ccb6f28c2e3d8c8cd6b8a7369d851a56c/3221880/device-tests/jenkins-results/tests/index.html) ✅

# :tada: All 113 tests passed :tada:


> This ain't a BackPort
7dc56e3 BACKPORT: dm bufio: introduce a global cache replacement by Mikulas Patocka · 8 weeks ago
b9fd9eb BACKPORT: dm bufio: remove old-style buffer cleanup by Mikulas Patocka · 8 weeks ago
6d453eb BACKPORT: dm bufio: introduce a global queue by Mikulas Patocka · 8 weeks ago
76ad885 BACKPORT: dm bufio: refactor adjust_total_allocated by Mikulas Patocka · 8 weeks ago
24d0cad BACKPORT: dm bufio: call adjust_total_allocated from __link_buffer and __unlink_buffer by Mikulas Patocka · 8 weeks ago


preciso terminar e partir pros próximos..


チェックしてます


test


根本就连不上，三百多块钱白花了


프론트 부분 상세 페이지를 만들었다.
opacity, border-radius를 사용하는 방법을 배웠다.


mexendo na responsividade, porque tava muit feiooooooooo essa pagina sem a meta viewport


Successfully deployed to following URLs:

* https://kybervirtualhackathon-2acw5zdgn.now.sh
* https://defizap.com
* https://kybervirtualhackathon.botforkybergang.now.sh
* https://kybervirtualhackathon-git-master.botforkybergang.now.sh


<details>

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

InterpreterError at template.tasks[0]: object keys must be strings

</details>


Successfully deployed to following URLs:

* https://portfolio-d9zcugqj7.now.sh
* https://yuwen-li.com
* https://www.yuwen-li.com
* https://portfolio.muzlee1113.now.sh
* https://portfolio-git-master.muzlee1113.now.sh


thanks


Successfully deployed to following URLs:

* https://super8express-jw415aq8m.now.sh
* https://super8express.now.sh
* https://super8express.super8express.now.sh
* https://super8express-git-master.super8express.now.sh


Successfully deployed to following URLs:

* https://to-do-app-17338l9t6.now.sh
* https://to-do-app.marchenkoulya26.now.sh
* https://to-do-app-git-master.marchenkoulya26.now.sh


Build version: __`3.3.0-master.920`__ :crossed_fingers: [`master`](https://github.com/streamich/md-mdast/tree/master) on [*CircleCI*](https://circleci.com/gh/streamich/md-mdast/920) :tada:


Thank you for your patient answer. You have helped me a lot. Thank you very much！


Successfully deployed to following URLs:

* https://news-ssr-126b9tbq7.now.sh
* https://shipping-news.tech
* https://dnews.cloud
* https://news-ssr.kunukn.now.sh
* https://news-ssr-git-master.kunukn.now.sh


Successfully deployed to following URLs:

* https://apollo-server-demo-iyong67sr.now.sh
* https://apollo-server-demo.charliewilco.now.sh
* https://apollo-server-demo-git-master.charliewilco.now.sh


[R/alignment_params_to_posterior_trees.R:78:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/check_sim_twin_alignment_function.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
check_sim_twin_alignment_function <- function(sim_twin_alignment_function) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:20:5:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/check_sim_twin_alignment_function.R#L20) *style:* **Commented code should be removed.**
```r
  # n_args <- stringr::str_count(string = arguments, pattern = ",") + 1
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/check_sim_twin_alignment_function.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
  #     "'sim_twin_alignment_function' must be a function with two arguments. \n",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:23:21:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/check_sim_twin_alignment_function.R#L23) *warning:* **no visible global function definition for ‘get_default_sim_true_alignment_function’**
```r
  true_alignment <- get_default_sim_true_alignment_function()(twin_phylogeny)
                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/check_sim_twin_alignment_function.R:56:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/check_sim_twin_alignment_function.R#L56) *style:* **Lines should not be more than 80 characters.**
```r
        "'sim_twin_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_params.R:53:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/create_alignment_params.R#L53) *style:* **Lines should not be more than 80 characters.**
```r
  sim_true_alignment_function = pirouette::get_default_sim_true_alignment_function(),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment_params.R:87:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/create_alignment_params.R#L87) *style:* **Lines should not be more than 80 characters.**
```r
  sim_true_alignment_function = pirouette::get_default_sim_true_alignment_function(),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:12:3:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/create_alignment.R#L116) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_twin_alignment_with_standard_site_model_raw <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_alignment.R:145:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/create_sim_yule_twin_tree_function.R#L23) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_sim_yule_twin_tree_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/create_twin_alignment_with_standard_site_model.R:14:3:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/create_twin_alignment_with_standard_site_model.R#L14) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/create_twin_alignment_with_standard_site_model.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/create_twin_alignment_with_standard_site_model.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
create_twin_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/est_evidences.R:35:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_alignment_sequences.R#L5) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/get_default_sim_true_alignment_function.R:3:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_default_sim_true_alignment_function.R#L3) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_default_sim_true_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_default_sim_twin_alignment_function.R:4:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_default_sim_twin_alignment_function.R#L4) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_default_sim_twin_alignment_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_pir_params_filenames.R:6:17:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_pir_params_filenames.R#L6) *warning:* **no visible global function definition for ‘init_pir_params’**
```r
  pir_params <- init_pir_params(pir_params)
                ^~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R:15:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_sim_true_alignment_with_linked_node_sub_site_model_function.R#L15) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_linked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_standard_site_model_function.R:21:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_sim_true_alignment_with_standard_site_model_function.R#L21) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_standard_site_model_function <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_sim_true_alignment_with_unlinked_node_sub_site_model_function.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_true_alignment_with_unlinked_node_sub_site_model_function <-
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L2) *warning:* **no visible binding for global variable ‘sim_twin_alignment_with_same_n_mutation’**
```r
  sim_twin_alignment_with_same_n_mutation
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_same_n_mutation_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_sim_twin_alignment_with_same_n_mutation_function.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_same_n_mutation_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_standard_site_model_function.R:2:3:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_sim_twin_alignment_with_standard_site_model_function.R#L2) *warning:* **no visible binding for global variable ‘create_twin_alignment_with_standard_site_model’**
```r
  create_twin_alignment_with_standard_site_model
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/get_sim_twin_alignment_with_standard_site_model_function.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/get_sim_twin_alignment_with_standard_site_model_function.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
get_sim_twin_alignment_with_standard_site_model_function <- function() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/pir_run_true_tree.R:8:3:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/sim_true_alignment_with_standard_site_model.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_standard_site_model.R:27:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/sim_true_alignment_with_standard_site_model.R#L27) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_standard_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment_with_unlinked_node_sub_site_model.R:12:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/sim_true_alignment_with_unlinked_node_sub_site_model.R#L12) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_true_alignment_with_unlinked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_true_alignment.R:13:3:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/sim_true_alignment.R#L13) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_linked_node_sub_site_model.R:4:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/sim_twin_alignment_with_linked_node_sub_site_model.R#L4) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_linked_node_sub_site_model <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:15:3:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/sim_twin_alignment_with_same_n_mutation.R#L15) *warning:* **no visible global function definition for ‘check_alignment’**
```r
  check_alignment(alignment)
  ^~~~~~~~~~~~~~~
```
[R/sim_twin_alignment_with_same_n_mutation.R:28:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/R/sim_twin_alignment_with_same_n_mutation.R#L28) *style:* **Variable and function names should not be longer than 30 characters.**
```r
sim_twin_alignment_with_same_n_mutation <- function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_experiments.R:83:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_experiments.R#L83) *style:* **Lines should not be more than 80 characters.**
```r
  cand_experiment_1$inference_model$mcmc <- cand_experiment_2$inference_model$mcmc
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:77:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_true_alignment_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(true_phylogeny = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:21:79:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_true_alignment_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(true_phylogeny = "irrelevant") { }
                                                                              ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:23:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_true_alignment_function.R#L23) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:75:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_true_alignment_function.R#L28) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                          ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:28:77:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_true_alignment_function.R#L28) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_true_alignment_function = function(invalid_name = "irrelevant") { }
                                                                            ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:9:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_true_alignment_function.R#L37) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:37:25:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_true_alignment_function.R#L37) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_true_alignment_function.R:39:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_true_alignment_function.R#L39) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_true_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_alignment_function.R:21:62:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L21) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:21:64:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L21) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(twin_phylogeny) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:27:62:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L27) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                             ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:27:64:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L27) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_alignment_function = function(true_alignment) { }
                                                               ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:9:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "irrelevant" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:36:24:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L36) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "irrelevant" }
                       ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:45:9:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L45) *style:* **Opening curly braces should never go on their own line and should always be followed by a new line.**
```r
      ) { "not a phylo" }
        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:45:25:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L45) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      ) { "not a phylo" }
                        ^
```
[tests/testthat/test-check_sim_twin_alignment_function.R:47:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_alignment_function.R#L47) *style:* **Lines should not be more than 80 characters.**
```r
    "'sim_twin_alignment_function' must be a function that returns an ape::DNAbin"
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-check_sim_twin_tree_function.R:21:66:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-check_sim_twin_tree_function.R#L35) *style:* **Closing curly-braces should always be on their own line, unless it's followed by an else.**
```r
      sim_twin_tree_function = function(true_phylogeny = "irrelevant") { "not a phylo" }
                                                                                ^
```
[tests/testthat/test-create_error_measure_params.R:29:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-create_twin_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:115:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-get_alignment_n_taxa.R#L115) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_alignment_n_taxa.R:116:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-get_alignment_n_taxa.R#L116) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-get_experiments_filenames.R:10:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-get_pir_params_filenames.R#L107) *style:* **Lines should not be more than 80 characters.**
```r
    expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-pir_run.R:125:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/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/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-sim_true_alignment_with_standard_site_model.R#L17) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_true_alignment.R:33:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-sim_true_alignment.R#L33) *style:* **Lines should not be more than 80 characters.**
```r
    sim_true_alignment_function = get_sim_true_alignment_with_linked_node_sub_site_model_function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_true_alignment.R:66:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-sim_true_alignment.R#L66) *style:* **Lines should not be more than 80 characters.**
```r
    sim_true_alignment_function = get_sim_true_alignment_with_unlinked_node_sub_site_model_function(
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[tests/testthat/test-sim_true_alignment.R:95:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-sim_true_alignment.R#L95) *style:* **Trailing blank lines are superfluous.**
```r

^
```
[tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R:19:1:](https://github.com/richelbilderbeek/pirouette/blob/802037ae67036b524fdfb46b0a7a06c69990f5e0/tests/testthat/test-sim_twin_alignment_with_same_n_mutation.R#L19) *style:* **Trailing blank lines are superfluous.**
```r

^
```


Successfully deployed to following URLs:

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还好没花钱

------------------ 原始邮件 ------------------
发件人: "fubuki2333"<notifications@github.com>;
发送时间: 2019年11月7日(星期四) 下午3:38
收件人: "getlantern/download"<download@noreply.github.com>;
抄送: "Subscribed"<subscribed@noreply.github.com>;
主题: Re: [getlantern/download] Update README.md (c2be0c3)

根本就连不上，三百多块钱白花了

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Some Java little projects, funny algorithms problems.


double in


Successfully deployed to following URLs:

* https://clem-lfmt8efiu.now.sh
* https://clem.jcada.now.sh
* https://clem-git-master.jcada.now.sh


Successfully deployed to following URLs:

* https://kybervirtualhackathon-9iu5qqobo.now.sh
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* https://news-ssr-git-master.kunukn.now.sh


even I want to write something here....


My prompt gets flooded with attempted plugin downloads which all fail as they don't exist. Most of the plugins originally set to load do not.

Here's a short vid showing what happens: https://asciinema.org/a/weGmDyeQ2Fk3WWfEmSUJt1aNe


Initial Commit


# 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)|


Мб from feature_extractor import FeatureExtractor?
Там ведь файл лежит в нашей папке, у меня не скомпилилось так.


@lazka maybe because it was merged? No?


> Why are we here discussing it here again and not where we already started the discussion?

Because it's implemented in *this* commit and you are not happy with it. Just look closer. It's not that large.
But it's not possible without a (public or private) way to retrieve the name lock status.

> What do you mean?

Locking works. I'm missing exceptions.


thanks


@Baitinq I made some minor improvements here and there. There are more stuff I could according to 'shellcheck' but I choose what to follow.


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we don't have any object/message that is empty when it was serialized? maybe is better to `return new T()`


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

I updated the Github team because of this commit.

- @dgasmith, @lnaden were 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)


官方公告 ： ONTK即将打造一个生态系统，这一次壹公链实施区块链应用（D.app）的落地，透过数字货币与壹公链核心Token（ONTK）引领高端科技真正地走进人们的生活中。

团队背景 ： Insource IT核心团队拥有大型企业管理，创业和投资经验，理念是不断发展和教育以及持续对团队的支持与信任。他们的学位背景几乎都位于俄罗斯，美国，英国，新加波和马来西亚。

Insource IT Solution 团队具有独特的创造力和独特的背景，让事业更上一层楼。

项目基本情况：ONE是一个无国界项目，由中国、马来西亚、新加坡、欧洲数个国家同时起步，累计经验、打磨平台。随着项目的推进，ONE将把技术研发中心和市场拓展全球化，辐射全亚洲、北美、东欧等。在其他区域

我们继续坚守最快的应用落地，最广泛的行业拓展，专注于区块链对各行各业的研发，为全球终端客户解决好“信任”的问题，运用区块链产业的变革，为整个生态获得更大的价值增值

媒体报道：暂时没有媒体报导过

收录的交易所：◦ BC Global Tech Limited IN Cayman
              ◦ 领衔全球的数字资产交易平台
              ◦ https://www.ezb.com/#/

Gas Limit : 6000(默认)


Successfully deployed to following URLs:

* https://portfolio-qhauc92lp.now.sh
* https://yuwen-li.com
* https://www.yuwen-li.com
* https://portfolio.muzlee1113.now.sh
* https://portfolio-git-master.muzlee1113.now.sh


pullshit


Copy of this build can be found at
https://www.mewbuilds.com/build/7ac2349697b2e51f053dd785ca60e1c2f57802c0/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmYP73ZDpg7tuQ6jr4JSnLkxdWPMHPPBVwxKSZXFrk2HXU
                       Virus Total analysis
                       https://www.virustotal.com/file/54fe71503fb707b0041b429934a7368cb58a11be4dfa9064e8a1fb866dcf2c5f/analysis/1573113539/


Successfully deployed to following URLs:

* https://sincerewines-cccaehi1m.now.sh
* https://sincerewines.now.sh
* https://www.sincerewines.com
* https://sincerewines.sincerewines.now.sh
* https://sincerewines-git-master.sincerewines.now.sh


I think `hasError: state => !!state.error` is better


Copy of this build can be found at
https://www.mewbuilds.com/build/866cf718d7efad2287eb6e8fc54bf7c00a48b0bb/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmfDJ57FbPaZwLhAstbtzF3gXwB1LRGgL43wwDZfbxSqP6
                       Virus Total analysis
                       https://www.virustotal.com/file/b62ec66ea25f72e5224392c8a336bbe9bc379acc009f5e8bdef2df2497624248/analysis/1573113652/


this is good


> this is good

ok


You’re awesome!


Successfully deployed to following URLs:

* https://kendraio-adapter-acw6hd0gq.now.sh
* https://kendraio-adapter.kendraio.now.sh
* https://kendraio-adapter-git-master.kendraio.now.sh


@web-flow


Successfully deployed to following URLs:

* https://tf-food-qjlw0gxg8.now.sh
* https://tf-food.quankun7.now.sh
* https://tf-food-git-master.quankun7.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)|


Hi, glad to be part of this team.. so I'm inquiring about the stack you have in mind for this project. it a really nice idea


Checkmarx scan results 07 Nov 2019 10:09 UTC +02:00

High
Medium
Low
Info

New
0
0
0
0

Recurrent
0
0
0
0

Fixed
0
0
0
0

 Open Viewer
Included commits

Commit ID	Owner

1e71c4b085217e0cab2013734fb62a6c80309419	@web-flow


Successfully deployed to following URLs:

* https://iwoka-task-5djpqoewz.now.sh
* https://iwoka-task-kappa-ruddy.now.sh
* https://iwoka-task.a133xz.now.sh
* https://iwoka-task-git-master.a133xz.now.sh


Successfully deployed to following URLs:

* https://rolandoio-1fbtpbj4b.now.sh
* https://rolando.io
* https://rolandoio.rlx310.now.sh
* https://rolandoio-git-master.rlx310.now.sh


Successfully deployed to following URLs:

* https://hueup-e9yhfbax8.now.sh
* https://hueup.matrixweb.de
* https://hueup.knister-peter.now.sh
* https://hueup-git-master.knister-peter.now.sh


Why would you think that? Tesseract may be special (and I'd like to see a reference into actual code for that yet).

But I fail to see anything wrong with `bbox_from_polygon` or `bbox_from_xywh`. An image with 1000 pixels in width starts at `x==0` (i.e. to the left of the first pixel) and ends at `x==1000` (i.e. to the left of the 1001st pixel, or equally, to the right of the 1000th pixel).


are this are test credentials??


Successfully deployed to following URLs:

* https://expressjs-opensource-r01udp4xx.now.sh
* https://expressjs-opensource.fast-start1.now.sh
* https://expressjs-opensource-git-master.fast-start1.now.sh


Ahhh... Updated to test args as well


Update


Fixed promote ?


Okay, the execution of actions in a visual mode was broken in case of enabled `incsearch`.

Thank you for the report. The fix will be released soon.


Successfully deployed to following URLs:

* https://interface-4ntf54ycw.now.sh
* https://interface.avantgarde-finance.now.sh
* https://interface-git-master.avantgarde-finance.now.sh


Thank you for Sharing....


Successfully deployed to following URLs:

* https://hostingguru-d9lzd1ymn.now.sh
* https://hostingguru.wiki
* https://hostingguru.joozty.now.sh
* https://hostingguru-git-master.joozty.now.sh


[Your benchmark job](https://github.com/JuliaLang/julia/commit/3b11bf3add57343073f02ecea13f9049600ea6bf#commitcomment-35841695) has completed - possible performance regressions were detected. A full report can be found [here](https://github.com/JuliaCI/BaseBenchmarkReports/blob/aa7896d6a57062bf83e452cdc855c5361416c4dc/daily_2019_11_07/report.md). cc @ararslan


Check if `fd` gets changed and bound to `INADDR_ANY` in server mode in `BIO_set_fd`.


Gghhhjji


I think here is a typing mistake. Shouldn't it be Guide.title(title)?


Change in `BIO_set_fd` will make this change redundant.


Check `getsockname` inside the condition and return error if it fails.


Successfully deployed to following URLs:

* https://hostingguru-l7187ig32.now.sh
* https://hostingguru.wiki
* https://hostingguru.joozty.now.sh
* https://hostingguru-git-master.joozty.now.sh


Observed 20% speedup in a simulation that uses polybell + polybell + wrapped custom potential with this change.


Successfully deployed to following URLs:

* https://pillar-3t12e5hp6.now.sh
* https://pillar.gives
* https://pillar.newmanoscar.now.sh
* https://pillar-git-master.newmanoscar.now.sh


Thank you for Sharing...


not yet.

On Thu, 7 Nov, 2019, 1:45 PM Shahnawaz Alam, <notifications@github.com>
wrote:

> Fixed promote ?
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <https://github.com/mkaraniya/BotHub/commit/b0741332c62309af744211e45b70f176c6413ac6?email_source=notifications&email_token=ALFSCSOOPVY2RPYUYK5DZK3QSPFBJA5CNFSM4JKC73E2YY3PNVWWK3TUL52HS4DFVVBW63LNNF2EG33NNVSW45FKMNXW23LFNZ2F62LEZYBCF3UU#commitcomment-35843732>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/ALFSCSMOW7ECFQGPDLKPEP3QSPFBJANCNFSM4JKC73EQ>
> .
>


Possibly move this block in `BIO_set_fd` as the state `addr_is_any` depends on the `fd`.


Добавление ссылки профиля.


Successfully deployed to following URLs:

* https://blog-wnwywrrzq.now.sh
* https://www.ahonn.me
* https://blog.ahonn.now.sh
* https://blog-git-master.ahonn.now.sh


Successfully deployed to following URLs:

* https://hostingguru-txosi53hs.now.sh
* https://hostingguru.wiki
* https://hostingguru.joozty.now.sh
* https://hostingguru-git-master.joozty.now.sh


Move at common place, at the top of file?


What about IPv6?


Successfully deployed to following URLs:

* https://free-fitness-mck3xczrd.now.sh
* https://free-fitness.by
* https://free-fitness.happylolonly.now.sh
* https://free-fitness-git-develop.happylolonly.now.sh


Guard IPv6 code under IPv6 macro.


@amalloy @kluever I see that these tests were removed, but AFAICT `check_api` is a valid directory inside this project, so I wondered if you could clarify for me why the tests were removed rather than moved to `check_api`? 🤔


Test after removing redundant `memset`.


Be consistent as in IPv6 case.


Copy of this build can be found at
https://www.mewbuilds.com/build/97073d19c896a06a1a6dff87a55c6bcdb1bbc389/index.html
                       https://www.cloudflare-ipfs.com/ipfs/QmQVHTN5z6hnUbBu5fMBXo2mRWJqnuriKRT7ycLRhCweKf
                       Virus Total analysis
                       https://www.virustotal.com/file/206bdae3d98d164de4920b2e53a6a59835928efefb41e673b96879dc11f4729e/analysis/1573115205/


Guard IPv6 code under IPv6 flag.


z


Sorry for not seeing the filenames in there.


Remove commented code.


你好具体怎么用能交一下么，怎么联系


<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/code-coverage:pull-request",
  "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 project/taskcluster/tc-github/production-2 does not have sufficient scopes and is missing the following scopes:

```
{
  "AnyOf": [
    {
      "AnyOf": [
        "queue:create-task:highest:proj-relman/ci",
        "queue:create-task:very-high:proj-relman/ci",
        "queue:create-task:high:proj-relman/ci",
        "queue:create-task:medium:proj-relman/ci",
        "queue:create-task:low:proj-relman/ci",
        "queue:create-task:very-low:proj-relman/ci",
        "queue:create-task:lowest:proj-relman/ci"
      ]
    },
    {
      "AnyOf": [
        "queue:create-task:proj-relman/ci",
        {
          "AllOf": [
            "queue:define-task:proj-relman/ci",
            "queue:task-group-id:taskcluster-github/dvLngIWfRUmfN4Q6sYk3KQ",
            "queue:schedule-task:taskcluster-github/dvLngIWfRUmfN4Q6sYk3KQ/IAPO49TXS1GJgrOCx_OcJw"
          ]
        }
      ]
    }
  ]
}
```

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:proj-relman/ci",
                "queue:create-task:very-high:proj-relman/ci",
                "queue:create-task:high:proj-relman/ci",
                "queue:create-task:medium:proj-relman/ci",
                "queue:create-task:low:proj-relman/ci",
                "queue:create-task:very-low:proj-relman/ci",
                "queue:create-task:lowest:proj-relman/ci"
              ]
            }
          ]
        },
        {
          "AnyOf": [
            "queue:create-task:proj-relman/ci",
            {
              "AllOf": [
                "queue:define-task:proj-relman/ci",
                "queue:task-group-id:taskcluster-github/dvLngIWfRUmfN4Q6sYk3KQ",
                "queue:schedule-task:taskcluster-github/dvLngIWfRUmfN4Q6sYk3KQ/IAPO49TXS1GJgrOCx_OcJw"
              ]
            }
          ]
        }
      ]
    }
  ]
}
```

---

* method:     createTask
* errorCode:  InsufficientScopes
* statusCode: 403
* time:       2019-11-07T08:28:31.464Z

</details>