Make the nlme test file work with testthat

3 files changed, 16 insertions, 22 deletions

diff --git a/test.log b/test.log
index 877d5193..09dd4c3f 100644
--- a/test.log
+++ b/test.log
@@ -7,42 +7,33 @@ Testing mkin
 ✔ |   4       | Fitting the SFORB model [1.7 s]
 ✔ |   5       | Calculation of Akaike weights
 ✔ |  10       | Confidence intervals and p-values [9.4 s]
-✔ |  14       | Error model fitting [37.5 s]
+✔ |  14       | Error model fitting [38.4 s]
 ✔ |   6       | Test fitting the decline of metabolites from their maximum [0.8 s]
 ✔ |   1       | Fitting the logistic model [0.9 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
-✔ |  12       | Special cases of mkinfit calls [2.3 s]
+✔ |  12       | Special cases of mkinfit calls [2.4 s]
 ✔ |   9       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.3 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.1 s]
-✖ |   0 1     | Nonlinear mixed-effects models [1.3 s]
-────────────────────────────────────────────────────────────────────────────────
-test_nlme.R:37: error: nlme_function works correctly
-konnte Funktion "nlme_f" nicht finden
-Backtrace:
- 1. nlme::nlme(...) tests/testthat/test_nlme.R:37:2
- 2. nlme::nlme.formula(...)
- 3. [ base::eval(...) ] with 1 more call
- 5. [ base::eval(...) ] with 1 more call
-────────────────────────────────────────────────────────────────────────────────
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.2 s]
+✔ |   3       | Nonlinear mixed-effects models [2.1 s]
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
 ✔ |   3       | Summary
 ✔ |  11       | Plotting [0.6 s]
 ✔ |   4       | AIC calculation
 ✔ |   2       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.5 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.0 s]
-✔ |   7     1 | Hypothesis tests [31.9 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s]
+✔ |   7     1 | Hypothesis tests [34.0 s]
 ────────────────────────────────────────────────────────────────────────────────
 test_tests.R:60: skip: We can do a likelihood ratio test using an update specification
 Reason: This errors out if called by testthat while it works in a normal R session
 ────────────────────────────────────────────────────────────────────────────────
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 111.4 s
+Duration: 115.8 s
 
-OK:       138
-Failed:   1
+OK:       141
+Failed:   0
 Warnings: 0
 Skipped:  1
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index f492a57f..118f61f4 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2020-04-07
+Date: 2020-04-08
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index b3c41f00..31db92e1 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -26,7 +26,11 @@ test_that("nlme_function works correctly", {
 
   mean_dp <- mean_degparms(f)
   grouped_data <- nlme_data(f)
+
   nlme_f <- nlme_function(f)
+  # The following assignment was introduced for nlme as evaluated by testthat
+  # to find the function
+  assign("nlme_f", nlme_f, pos = globalenv())
 
   m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
     data = grouped_data,
@@ -58,6 +62,5 @@ test_that("nlme_function works correctly", {
   m_nlme_mkin_up_2 <- update(m_nlme_mkin, random = parent_0 ~ 1)
   expect_equal(m_nlme_raw_up_2$coefficients, m_nlme_mkin_up_2$coefficients)
 
-  # update(m_nlme_mkin) # works
-
+  expect_silent(tmp <- update(m_nlme_mkin))
 })