Expose unhelpful error

[richelbilderbeek]

Hi @Giappo,

A couple of days ago, my becosys package build broke. The reason is that this code gives an unhelpful error message, since four days. Here is the reprex:

library(mbd)
set.seed(44)
mbd_ml(
  brts = c(3.0, 2.0),
  start_pars = c(0.3, 0.1, 0.0, 0.0),
  true_pars = c(0.3, 0.1, 0.0, 0.0),
  optim_ids = c(TRUE, TRUE, FALSE, FALSE),
  cond = 1,
  n_0 = 2
)

In this Pull Request, I've added a test that will break the build, to verify this is indeed an error. I put the test below one of your tests, that test in a very similar parameter setting.

What I would expect, is that this test either works, or gives a helpful error message.

I hope this extra test helps to improve mbd.

For more details (e.g. which mbd commit broke the becosys build), see this Issue.

Good luck 👍

[lintr-bot]

R/mbd_main_utils.R:13:3: warning: local variable ‘pkg_name’ assigned but may not be used

​  pkg_name <- get_pkg_name() # nolint internal function
  ^~~~~~~~

R/mbd_main_utils.R:13:15: warning: no visible global function definition for ‘get_pkg_name’

​  pkg_name <- get_pkg_name() # nolint internal function
              ^~~~~~~~~~~~

[richelbilderbeek]

Instead of waiting, the error can already be viewed here

[lintr-bot]

R/mbd_loglik_utils.R:39:1: style: Lines should not be more than 80 characters.

​    matrix_a[s + 2, dst] <- matrix_a[s, src] + matrix_a[s + 1, src] # check here! TODO
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/mbd_loglik_utils.R:150:1: style: functions should have cyclomatic complexity of less than 15, this has 16.

​create_a_slow <- function(
^

R/mbd_loglik_utils.R:181:1: style: Lines should not be more than 80 characters.

​        if (is.nan(a_matrix_mn) || a_matrix_mn == 0 || is.infinite(a_matrix_mn)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mbd_matrices.R:238:1: style: functions should have cyclomatic complexity of less than 15, this has 17.

​test_that("a_matrix: hardcore case", {
^

tests/testthat/test-mbd_matrices.R:254:13: warning: Avoid 1:nrow(...) expressions, use seq_len.

​  for (i in 1:nrow(coords)) {
            ^

tests/testthat/test-mbd_matrices.R:261:7: style: Commented code should be removed.

​    # sum(2 ^ j * choose(k, j) * choose(n, m - n - j))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mbd_matrices.R:292:7: style: Commented code should be removed.

​    # sum(2 ^ j * choose(k, j) * choose(n, m - n - j))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[lintr-bot]

R/mbd_loglik_utils.R:39:1: style: Lines should not be more than 80 characters.

​    matrix_a[s + 2, dst] <- matrix_a[s, src] + matrix_a[s + 1, src] # check here! TODO
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/mbd_loglik_utils.R:150:1: style: functions should have cyclomatic complexity of less than 15, this has 16.

​create_a_slow <- function(
^

R/mbd_loglik_utils.R:181:1: style: Lines should not be more than 80 characters.

​        if (is.nan(a_matrix_mn) || a_matrix_mn == 0 || is.infinite(a_matrix_mn)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/mbd_main_utils.R:13:3: warning: local variable ‘pkg_name’ assigned but may not be used

​  pkg_name <- get_pkg_name() # nolint internal function
  ^~~~~~~~

R/mbd_main_utils.R:13:15: warning: no visible global function definition for ‘get_pkg_name’

​  pkg_name <- get_pkg_name() # nolint internal function
              ^~~~~~~~~~~~

tests/testthat/test-mbd_matrices.R:238:1: style: functions should have cyclomatic complexity of less than 15, this has 17.

​test_that("a_matrix: hardcore case", {
^

tests/testthat/test-mbd_matrices.R:254:13: warning: Avoid 1:nrow(...) expressions, use seq_len.

​  for (i in 1:nrow(coords)) {
            ^

tests/testthat/test-mbd_matrices.R:261:7: style: Commented code should be removed.

​    # sum(2 ^ j * choose(k, j) * choose(n, m - n - j))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test-mbd_matrices.R:292:7: style: Commented code should be removed.

​    # sum(2 ^ j * choose(k, j) * choose(n, m - n - j))
      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~