Closed Giappo closed 4 years ago
R/check_pir_out.R:17:1: style: functions should have cyclomatic complexity of less than 15, this has 17.
check_pir_out <- function( ^
R/create_alignment_with_std_site_model.R:5:1: style: Variable and function names should not be longer than 30 characters.
create_alignment_with_std_site_model <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/create_all_experiments.R:24:1: style: functions should have cyclomatic complexity of less than 15, this has 30.
create_all_experiments <- function( ^
R/create_copy_twin_tree_from_true_fun.R:21:1: style: Variable and function names should not be longer than 30 characters.
create_copy_twin_tree_from_true_fun <- function() { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/est_evidences.R:35:1: style: functions should have cyclomatic complexity of less than 15, this has 20.
est_evidences <- function( ^
R/get_sim_true_alignment_with_lns_site_model_fun.R:23:1: style: Variable and function names should not be longer than 30 characters.
get_sim_true_alignment_with_lns_site_model_fun <- ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/get_sim_true_alignment_with_std_site_model_fun.R:21:1: style: Variable and function names should not be longer than 30 characters.
get_sim_true_alignment_with_std_site_model_fun <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/get_sim_true_alignment_with_uns_site_model_fun.R:20:1: style: Variable and function names should not be longer than 30 characters.
get_sim_true_alignment_with_uns_site_model_fun <- ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/get_sim_twin_alignment_with_same_n_mutation_fun.R:29:1: style: Variable and function names should not be longer than 30 characters.
get_sim_twin_alignment_with_same_n_mutation_fun <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/get_sim_twin_alignment_with_std_site_model_fun.R:30:1: style: Variable and function names should not be longer than 30 characters.
get_sim_twin_alignment_with_std_site_model_fun <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/select_candidate_evidences.R:25:1: style: functions should have cyclomatic complexity of less than 15, this has 20.
select_candidate_evidences <- function( ^
R/sim_alignment_with_std_site_model.R:15:1: style: Variable and function names should not be longer than 30 characters.
sim_alignment_with_std_site_model <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/sim_true_alignment_with_lns_site_model.R:12:1: style: Variable and function names should not be longer than 30 characters.
sim_true_alignment_with_lns_site_model <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/sim_true_alignment_with_std_site_model.R:21:1: style: Variable and function names should not be longer than 30 characters.
sim_true_alignment_with_std_site_model <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/sim_true_alignment_with_uns_site_model.R:13:1: style: Variable and function names should not be longer than 30 characters.
sim_true_alignment_with_uns_site_model <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/sim_twin_alignment_with_lns_site_model.R:11:1: style: Variable and function names should not be longer than 30 characters.
sim_twin_alignment_with_lns_site_model <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/sim_twin_alignment_with_same_n_mutation.R:30:1: style: Variable and function names should not be longer than 30 characters.
sim_twin_alignment_with_same_n_mutation <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/sim_twin_alignment_with_std_site_model_raw.R:5:1: style: Variable and function names should not be longer than 30 characters.
sim_twin_alignment_with_std_site_model_raw <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/sim_twin_alignment_with_std_site_model.R:29:1: style: Variable and function names should not be longer than 30 characters.
sim_twin_alignment_with_std_site_model <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/sim_twin_alignment_with_uns_site_model.R:11:1: style: Variable and function names should not be longer than 30 characters.
sim_twin_alignment_with_uns_site_model <- function( ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/update_pirouette.R:4:1: style: Lines should not be more than 80 characters.
devtools::install_github("richelbilderbeek/babette", quiet = TRUE, dependencies = TRUE, upgrade = "always") ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
R/update_pirouette.R:5:1: style: Lines should not be more than 80 characters.
devtools::install_github("richelbilderbeek/mcbette", quiet = TRUE, dependencies = TRUE, upgrade = "always") ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tests/testthat/test-check_sim_twin_tree_fun.R:53:25: style: Variable and function name style should be snake_case.
true_phylogeny2$tip.label <- paste0(true_phylogeny$tip.label, "h") ^~~~~~~~~
tests/testthat/test-get_experiments_filenames.R:38:1: style: Lines should not be more than 80 characters.
expect_true(experiment$inference_model$mcmc$tracelog$filename %in% filenames) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tests/testthat/test-get_pir_params_filenames.R:47:1: style: Lines should not be more than 80 characters.
tests/testthat/test-get_pir_params_filenames.R:71:1: style: Lines should not be more than 80 characters.
tests/testthat/test-get_pir_params_filenames.R:114:1: style: Lines should not be more than 80 characters.
R/check_pir_out.R:17:1: style: functions should have cyclomatic complexity of less than 15, this has 17.
R/create_alignment_with_std_site_model.R:5:1: style: Variable and function names should not be longer than 30 characters.
R/create_all_experiments.R:24:1: style: functions should have cyclomatic complexity of less than 15, this has 30.
R/create_copy_twin_tree_from_true_fun.R:21:1: style: Variable and function names should not be longer than 30 characters.
R/est_evidences.R:35:1: style: functions should have cyclomatic complexity of less than 15, this has 20.
R/get_sim_true_alignment_with_lns_site_model_fun.R:23:1: style: Variable and function names should not be longer than 30 characters.
R/get_sim_true_alignment_with_std_site_model_fun.R:21:1: style: Variable and function names should not be longer than 30 characters.
R/get_sim_true_alignment_with_uns_site_model_fun.R:20:1: style: Variable and function names should not be longer than 30 characters.
R/get_sim_twin_alignment_with_same_n_mutation_fun.R:29:1: style: Variable and function names should not be longer than 30 characters.
R/get_sim_twin_alignment_with_std_site_model_fun.R:30:1: style: Variable and function names should not be longer than 30 characters.
R/select_candidate_evidences.R:25:1: style: functions should have cyclomatic complexity of less than 15, this has 20.
R/sim_alignment_with_std_site_model.R:15:1: style: Variable and function names should not be longer than 30 characters.
R/sim_true_alignment_with_lns_site_model.R:12:1: style: Variable and function names should not be longer than 30 characters.
R/sim_true_alignment_with_std_site_model.R:21:1: style: Variable and function names should not be longer than 30 characters.
R/sim_true_alignment_with_uns_site_model.R:13:1: style: Variable and function names should not be longer than 30 characters.
R/sim_twin_alignment_with_lns_site_model.R:11:1: style: Variable and function names should not be longer than 30 characters.
R/sim_twin_alignment_with_same_n_mutation.R:30:1: style: Variable and function names should not be longer than 30 characters.
R/sim_twin_alignment_with_std_site_model_raw.R:5:1: style: Variable and function names should not be longer than 30 characters.
R/sim_twin_alignment_with_std_site_model.R:29:1: style: Variable and function names should not be longer than 30 characters.
R/sim_twin_alignment_with_uns_site_model.R:11:1: style: Variable and function names should not be longer than 30 characters.
R/update_pirouette.R:4:1: style: Lines should not be more than 80 characters.
R/update_pirouette.R:5:1: style: Lines should not be more than 80 characters.
tests/testthat/test-check_sim_twin_tree_fun.R:53:25: style: Variable and function name style should be snake_case.
tests/testthat/test-get_experiments_filenames.R:38:1: style: Lines should not be more than 80 characters.
tests/testthat/test-get_pir_params_filenames.R:47:1: style: Lines should not be more than 80 characters.
tests/testthat/test-get_pir_params_filenames.R:71:1: style: Lines should not be more than 80 characters.
tests/testthat/test-get_pir_params_filenames.R:114:1: style: Lines should not be more than 80 characters.