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-rw-r--r--tests/testthat/setup_script.R22
-rw-r--r--tests/testthat/test_saemix_parent.R2
2 files changed, 16 insertions, 8 deletions
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index c554800d..2448886d 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -2,17 +2,23 @@ require(mkin)
require(testthat)
# Per default (on my box where I set NOT_CRAN in .Rprofile) use all cores minus one
+# Otherwise (CRAN check systems) use the allowed maximum of two cores
if (identical(Sys.getenv("NOT_CRAN"), "true")) {
n_cores <- parallel::detectCores() - 1
} else {
- n_cores <- 1
+ n_cores <- 2
}
# Use the two available cores on travis
if (Sys.getenv("TRAVIS") != "") n_cores = 2
-# On Windows we would need to make a cluster first
-if (Sys.info()["sysname"] == "Windows") n_cores = 1
+# On Windows we need to make a cluster, or use one core
+if (Sys.info()["sysname"] == "Windows") {
+ cl <- parallel::makePSOCKcluster(n_cores)
+ n_cores = 1
+} else {
+ cl <- parallel::makeForkCluster(n_cores)
+}
# Very simple example fits
f_1_mkin_trans <- mkinfit("SFO", FOCUS_2006_A, quiet = TRUE)
@@ -24,7 +30,7 @@ models <- c("SFO", "FOMC", "DFOP", "HS")
fits <- suppressWarnings( # FOCUS A FOMC was, it seems, in testthat output
mmkin(models,
list(FOCUS_A = FOCUS_2006_A, FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
- quiet = TRUE, cores = n_cores))
+ quiet = TRUE, cluster = cl))
# One metabolite
SFO_SFO <- mkinmod(parent = mkinsub("SFO", to = "m1"),
@@ -82,13 +88,14 @@ fit_tc_1 <- mkinfit(m_synth_SFO_lin, SFO_lin_a, error_model = "tc", quiet = TRUE
error_model_algorithm = "threestep")
# Mixed model fits
-mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_cores)
-mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores,
+mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cluster = cl)
+mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cluster = cl,
error_model = "tc")
DFOP_SFO <- mkinmod(parent = mkinsub("DFOP", "m1"),
m1 = mkinsub("SFO"), quiet = TRUE)
-mmkin_dfop_sfo <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_dfop_sfo, quiet = TRUE, cores = n_cores,
+mmkin_dfop_sfo <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_dfop_sfo, quiet = TRUE,
+ cluster = cl,
control = list(eval.max = 500, iter.max = 400),
error_model = "tc")
@@ -105,3 +112,4 @@ dfop_saem_1 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "mkin",
saem_dfop_sfo_m <- saem(mmkin_dfop_sfo, transformations = "mkin", quiet = TRUE)
saem_dfop_sfo_s <- saem(mmkin_dfop_sfo, transformations = "saemix", quiet = TRUE)
+parallel::stopCluster(cl)
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index 31605931..7fbecd0c 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -15,7 +15,7 @@ test_that("Parent fits using saemix are correctly implemented", {
expect_silent(print(illparms(sfo_saem_1_reduced)))
# We cannot currently do the fit with completely fixed initial values
- mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100))
+ mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100), cluster = NULL, cores = n_cores)
sfo_saem_3 <- expect_error(saem(mmkin_sfo_2, quiet = TRUE), "at least two parameters")
# We get an error if we do not supply a suitable model specification

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