From 8252d2893622ade20f1baf9fcdd9a67d71472954 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Fri, 10 Feb 2023 18:03:27 +0100 Subject: [PATCH] ML and integration tests don't run on CRAN due to speed [run ci] --- tests/testthat/test-DAISIE_ML1.R | 3 ++- tests/testthat/test-DAISIE_ML2.R | 3 ++- tests/testthat/test-DAISIE_ML4.R | 1 + tests/testthat/test-DAISIE_MW_ML.R | 2 +- tests/testthat/test-DAISIE_loglik_CS.R | 9 +++++++-- tests/testthat/test-DAISIE_loglik_IW_solver.R | 4 ++-- tests/testthat/test-integration_DAISIE.R | 4 ++++ 7 files changed, 19 insertions(+), 7 deletions(-) diff --git a/tests/testthat/test-DAISIE_ML1.R b/tests/testthat/test-DAISIE_ML1.R index 2a11295f..4aa7def5 100644 --- a/tests/testthat/test-DAISIE_ML1.R +++ b/tests/testthat/test-DAISIE_ML1.R @@ -2,7 +2,7 @@ context("DAISIE_ML1") test_that("use", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") - + skip_on_cran() data(Galapagos_datalist) datalist <- Galapagos_datalist initparsopt <- c(2.5, 2.7, 20, 0.009, 1.01) @@ -39,6 +39,7 @@ test_that("use", { test_that("abuse", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") + skip_on_cran() utils::data(Galapagos_datalist) datalist <- Galapagos_datalist initparsopt <- c(2.5, 2.7, 20, 0.009, 1.01) diff --git a/tests/testthat/test-DAISIE_ML2.R b/tests/testthat/test-DAISIE_ML2.R index 3d33840a..0d64954e 100644 --- a/tests/testthat/test-DAISIE_ML2.R +++ b/tests/testthat/test-DAISIE_ML2.R @@ -1,6 +1,6 @@ test_that("use", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") - + skip_on_cran() utils::data(Macaronesia_datalist, package = "DAISIE") invisible(capture.output( tested_MLE <- DAISIE_ML2( @@ -59,6 +59,7 @@ test_that("use", { test_that("abuse", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") + skip_on_cran() expect_error(tested_MLE <- DAISIE:::DAISIE_ML2( datalist = "nonsense", initparsopt = c( diff --git a/tests/testthat/test-DAISIE_ML4.R b/tests/testthat/test-DAISIE_ML4.R index 9449ba2a..435ec184 100644 --- a/tests/testthat/test-DAISIE_ML4.R +++ b/tests/testthat/test-DAISIE_ML4.R @@ -19,6 +19,7 @@ test_that("DAISIE_ML4 is silent and produces correct output", { test_that("DAISIE_loglik_all_choosepar4 is silent and produces correct output", { utils::data(Galapagos_datalist) skip_if(Sys.getenv("CI") == "", message = "Run only on CI") + skip_on_cran() # Throws warnings and DLSODES output invisible(capture.output(suppressWarnings( output <- DAISIE_loglik_all_choosepar4( diff --git a/tests/testthat/test-DAISIE_MW_ML.R b/tests/testthat/test-DAISIE_MW_ML.R index 875dfc93..23b55798 100644 --- a/tests/testthat/test-DAISIE_MW_ML.R +++ b/tests/testthat/test-DAISIE_MW_ML.R @@ -1,7 +1,7 @@ test_that("DAISIE_MW_ML produces correct output", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") - + skip_on_cran() utils::data(archipelagos41) diff --git a/tests/testthat/test-DAISIE_loglik_CS.R b/tests/testthat/test-DAISIE_loglik_CS.R index 1de5544d..bb55aba9 100644 --- a/tests/testthat/test-DAISIE_loglik_CS.R +++ b/tests/testthat/test-DAISIE_loglik_CS.R @@ -1,5 +1,6 @@ test_that("DAISIE_loglik_CS_choice produces correct output for CS_version 1", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") + skip_on_cran() pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010) pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04, 1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01) @@ -21,6 +22,7 @@ test_that("DAISIE_loglik_CS_choice produces correct output for CS_version 1", { test_that("DAISIE_loglik_CS_choice produces correct output for relaxed-rate model (CS_version = 2)", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") + skip_on_cran() pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010) pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04, 1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01) @@ -46,7 +48,7 @@ test_that("DAISIE_loglik_CS_choice produces correct output for relaxed-rate test_that("DAISIE_loglik_CS_choice produces same output for CS_version = 0 (with M = 1) and CS_version = 1 ", { - + skip_on_cran() skip_if(Sys.getenv("CI") == "", message = "Run only on CI") pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010) pars2 <- c(100, 11, 0, 0, NA, 0.0e+00, 1.0e-04, @@ -77,6 +79,7 @@ test_that("DAISIE_loglik_CS_choice produces same output for CS_version = 0 test_that("DAISIE_loglik_all produces correct output for relaxed-rate model", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") + skip_on_cran() utils::data(Galapagos_datalist) invisible(capture.output(suppressWarnings( loglik <- DAISIE::DAISIE_loglik_all( @@ -98,6 +101,7 @@ test_that("DAISIE_loglik_all produces correct output for relaxed-rate model", { test_that("DAISIE_loglik produces correct output", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") + skip_on_cran() output <- DAISIE_loglik(pars1 = c(2.061154e-09, 2.683455e+00, 1.000000e+01, 9.332070e-03, 1.010073e+00), pars2 = c(100, 0, 0, 0, NA), @@ -115,7 +119,7 @@ test_that("DAISIE_loglik produces correct output", { test_that("DAISIE_loglik_all produces same output for CS_version 0 and 1 with and without conditioning", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") - + skip_on_cran() utils::data(Galapagos_datalist) Galapagos_datalist2 <- Galapagos_datalist for(i in 2:9) { @@ -162,6 +166,7 @@ test_that("DAISIE_loglik_all produces same output for CS_version 0 and 1 with test_that("DAISIE_loglik_CS_choice produces equivalent output for ODEINT RKCK54 and deSolve lsodes", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") + skip_on_cran() pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010) pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04, 1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01) diff --git a/tests/testthat/test-DAISIE_loglik_IW_solver.R b/tests/testthat/test-DAISIE_loglik_IW_solver.R index 30c68384..c7013f37 100644 --- a/tests/testthat/test-DAISIE_loglik_IW_solver.R +++ b/tests/testthat/test-DAISIE_loglik_IW_solver.R @@ -1,6 +1,6 @@ test_that("IW and CS loglik is same when K = Inf", { skip_if(Sys.getenv("CI") == "", message = "Run only on CI") - + skip_on_cran() utils::data(Galapagos_datalist, package = "DAISIE") pars1 <- c(0.35, 0.3, Inf, 0.001, 0.3) pars2 <- c(120, 11, 0, 1) @@ -51,7 +51,7 @@ test_that("loglik IW various solver options give similar results", { # Test is not included in coverage due to issue with running loglik_IW # code from covr::package_coverage() testthat::skip_on_covr() - + skip_on_cran() utils::data(frogs_datalist, package = "DAISIE") pars1 <- c(0.2, 0.1, 1000.1, 0.001, 0.3) pars2 <- c(40, 11, 0, 0) diff --git a/tests/testthat/test-integration_DAISIE.R b/tests/testthat/test-integration_DAISIE.R index c6b1e5c7..c6923be8 100644 --- a/tests/testthat/test-integration_DAISIE.R +++ b/tests/testthat/test-integration_DAISIE.R @@ -63,6 +63,7 @@ test_that("clade specific rate-shift loglik works", { test_that("IW and CS loglik is same when K = Inf", { skip_if(Sys.getenv("CI") == "" && !(Sys.getenv("USERNAME") == "rampa"), message = "Run only on CI") + skip_on_cran() data(Galapagos_datalist, package = "DAISIE") pars1 <- c(0.35, 0.3, Inf, 0.001, 0.3) pars2 <- c(80, 11, 1, 0) @@ -103,6 +104,7 @@ test_that("IW and CS loglik is same when K = Inf", { test_that("DAISIE_ML simple case works", { skip_if(Sys.getenv("CI") == "" && !(Sys.getenv("USERNAME") == "rampa"), message = "Run only on CI") + skip_on_cran() expected_mle <- data.frame( lambda_c = 2.583731356303842, mu = 2.708828027514834, @@ -131,6 +133,7 @@ test_that("DAISIE_ML simple case works", { test_that("DAISIE_ML simple case works with zero probability of initial presence", { skip_if(Sys.getenv("CI") == "" && !(Sys.getenv("USERNAME") == "rampa"), message = "Run only on CI") + skip_on_cran() expected_mle <- data.frame( lambda_c = 2.583731356303842, mu = 2.708828027514834, @@ -190,6 +193,7 @@ test_that("DAISIE_ML simple case works with estimating probability of initial presence", { skip_if(Sys.getenv("CI") == "" && !(Sys.getenv("USERNAME") == "rampa"), message = "Run only on CI") + skip_on_cran() expected_mle <- data.frame( lambda_c = 2.54079308283855,