From 3cddc58e6fcdd5341b354dc5b5f784ec8190f62b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 14 Mar 2022 15:41:56 +0100 Subject: Reduce check time for CRAN, release --- tests/testthat/setup_script.R | 14 -------------- tests/testthat/test_analytical.R | 7 ++----- tests/testthat/test_plot.R | 14 ++++++++++++++ tests/testthat/test_saemix_parent.R | 1 + 4 files changed, 17 insertions(+), 19 deletions(-) (limited to 'tests') diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 10696082..8ffe0b9d 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -202,17 +202,3 @@ dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix") saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE) saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE) -# UBA datasets -ds_uba <- lapply(experimental_data_for_UBA_2019[6:10], - function(x) subset(x$data[c("name", "time", "value")])) -names(ds_uba) <- paste("Dataset", 6:10) -sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"), - A1 = mkinsub("SFO"), quiet = TRUE) -dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"), - A1 = mkinsub("SFO"), quiet = TRUE) -f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba), - ds_uba, quiet = TRUE, cores = n_cores) -f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ]) - -f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix") -f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix") diff --git a/tests/testthat/test_analytical.R b/tests/testthat/test_analytical.R index 66fb1ace..e6cb7ed3 100644 --- a/tests/testthat/test_analytical.R +++ b/tests/testthat/test_analytical.R @@ -1,9 +1,7 @@ context("Analytical solutions for coupled models") -# We do not want the warnings due to non-normality of residuals here -warn_option <- options(warn=-1) - test_that("The analytical solutions for SFO-SFO are correct", { + skip_on_cran() # No sink, no formation fractions SFO_SFO_nosink <- mkinmod( parent = mkinsub("SFO", to = "m1", sink = FALSE), @@ -50,6 +48,7 @@ test_that("The analytical solutions for SFO-SFO are correct", { }) test_that("The analytical solution for DFOP-SFO are correct", { + skip_on_cran() # With formation fraction f_dfop_sfo_analytical <- mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE) @@ -61,5 +60,3 @@ test_that("The analytical solution for DFOP-SFO are correct", { tolerance = 5e-6 ) }) - -options(warn = warn_option$warn) diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R index 4f484cf3..58a00662 100644 --- a/tests/testthat/test_plot.R +++ b/tests/testthat/test_plot.R @@ -30,6 +30,20 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", { plot_err_sfo_sfo <- function() plot_err(f_sfo_sfo_desolve) vdiffr::expect_doppelganger("plot_err for FOCUS D", plot_err_sfo_sfo) + # UBA datasets + ds_uba <- lapply(experimental_data_for_UBA_2019[6:10], + function(x) subset(x$data[c("name", "time", "value")])) + names(ds_uba) <- paste("Dataset", 6:10) + sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"), + A1 = mkinsub("SFO"), quiet = TRUE) + dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"), + A1 = mkinsub("SFO"), quiet = TRUE) + f_uba_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo_uba), + ds_uba, quiet = TRUE, cores = n_cores) + f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin["DFOP-SFO", ]) + + f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix") + plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed) vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin) diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R index 8beceba9..340db6f1 100644 --- a/tests/testthat/test_saemix_parent.R +++ b/tests/testthat/test_saemix_parent.R @@ -2,6 +2,7 @@ context("saemix parent models") test_that("Parent fits using saemix are correctly implemented", { + skip_on_cran() expect_error(saem(fits), "Only row objects") # Some fits were done in the setup script mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100)) -- cgit v1.2.1