Make saemix and corresponding tests optional

Address release critical check and test issues

1 files changed, 29 insertions, 23 deletions

diff --git a/test.log b/test.log
index 7a9c55ed..ead5a1c7 100644
--- a/test.log
+++ b/test.log
@@ -4,41 +4,47 @@ Testing mkin
 ✔ |  OK F W S | Context
 ✔ |   5       | AIC calculation
 ✔ |   2       | Export dataset for reading into CAKE
-✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s]
+✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [0.5 s]
-✔ |   7       | Fitting the SFORB model [3.6 s]
-✔ |   5       | Analytical solutions for coupled models [3.3 s]
+✔ |   7       | Fitting the SFORB model [4.0 s]
+✔ |   5       | Analytical solutions for coupled models [3.6 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  14       | Confidence intervals and p-values [1.2 s]
-✔ |  14       | Error model fitting [5.6 s]
+✔ |  14       | Confidence intervals and p-values [1.4 s]
+✔ |  14       | Error model fitting [6.8 s]
 ✔ |   5       | Time step normalisation
-✔ |   4       | Test fitting the decline of metabolites from their maximum [0.3 s]
-✔ |   1       | Fitting the logistic model [0.2 s]
-✔ |  33     1 | Nonlinear mixed effects models [28.7 s]
+✔ |   4       | Test fitting the decline of metabolites from their maximum [0.5 s]
+✔ |   1       | Fitting the logistic model [0.3 s]
+✔ |   5     3 | Nonlinear mixed-effects models [0.1 s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_mixed.R:143:3): saem results are reproducible for biphasic fits
-Reason: Fitting with saemix takes around 10 minutes when using deSolve
+Skip (test_mixed.R:4:3): Parent fits using saemix are correctly implemented
+Reason: !saemix_available is TRUE
+
+Skip (test_mixed.R:94:3): Print methods work
+Reason: !saemix_available is TRUE
+
+Skip (test_mixed.R:118:3): saem results are reproducible for biphasic fits
+Reason: !saemix_available is TRUE
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |   2       | Test dataset classes mkinds and mkindsg
-✔ |   1       | mkinfit features [0.3 s]
-✔ |  10       | Special cases of mkinfit calls [0.3 s]
+✔ |   1       | mkinfit features [0.4 s]
+✔ |  10       | Special cases of mkinfit calls [0.4 s]
 ✔ |   8       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.7 s]
-✔ |   9       | Nonlinear mixed-effects models [8.2 s]
-✔ |  16       | Plotting [1.9 s]
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [2.0 s]
+✔ |   9       | Nonlinear mixed-effects models [9.3 s]
+✔ |  14       | Plotting [2.0 s]
 ✔ |   4       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s]
-✔ |   4       | Summary [0.1 s]
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.8 s]
+✔ |   4       | Summary [0.2 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
-✔ |   9       | Hypothesis tests [7.3 s]
-✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5 s]
+✔ |   9       | Hypothesis tests [7.9 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.7 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 71.3 s
+Duration: 48.3 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
-● Fitting with saemix takes around 10 minutes when using deSolve (1)
+● !saemix_available is TRUE (3)
 
-[ FAIL 0 | WARN 0 | SKIP 1 | PASS 206 ]
+[ FAIL 0 | WARN 0 | SKIP 3 | PASS 176 ]