ML and integration tests don't run on CRAN due to speed [run ci]

rsetienne · Feb 10, 2023 · 8252d28 · 8252d28
1 parent c028bd3
commit 8252d28
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Showing 7 changed files with 19 additions and 7 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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,