diff --git a/DESCRIPTION b/DESCRIPTION index 860b496..7d16b66 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,7 +23,7 @@ URL: https://docs.ropensci.org/babette/ (website), https://github.com/ropensci/babette BugReports: https://github.com/ropensci/babette/issues Depends: - beautier (>= 2.6.11), + beautier (>= 2.6.12), beastier (>= 2.5), mauricer (>= 2.5.2), R (>= 3.5.0), diff --git a/tests/testthat/test-issues.R b/tests/testthat/test-issues.R index 6dd3d98..55784bc 100644 --- a/tests/testthat/test-issues.R +++ b/tests/testthat/test-issues.R @@ -1,6 +1,4 @@ test_that("use", { - - skip("#26") if (!is_beast2_installed()) return() filename <- get_babette_path( @@ -42,7 +40,6 @@ test_that("use", { }) test_that("use", { - skip("#26") if (!is_beast2_installed()) return() # Must be similar XML as # beautier::get_beautier_path("rln_and_tipdates_babette_issue_26.xml") @@ -112,3 +109,37 @@ test_that("clockRate.c ID and ClockPrior.c ID added twice", { beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() }) + + +test_that("Issue 106. Issue #106", { + + if (!is_on_ci()) return() + if (!is_beast2_installed()) return() + + fasta_filename <- beautier::get_fasta_filename() + sample_interval <- 10000 + mrca_pr <- beautier::create_mrca_prior( + taxa_names = beautier::get_taxa_names(fasta_filename), + is_monophyletic = TRUE, + mrca_distr = beautier::create_distr_normal(mean = 66, sigma = 1) + ) + + inf_model <- beautier::create_inference_model( + tree_prior = beautier::create_bd_tree_prior(), + clock_model = beautier::create_clock_model_rln(mean_clock_rate = ), + mcmc = beautier::create_mcmc( + chain_length = 1e6, + store_every = sample_interval + ), + mrca_prior = mrca_pr, + beauti_options = beautier::create_beauti_options_v2_6() + ) + + expect_silent( + babette::bbt_run_from_model( + fasta_filename = fasta_filename, + inference_model = inf_model, + beast2_options = beastier::create_beast2_options(rng_seed = 42) + ) + ) +})