Make saemix and corresponding tests optional

Address release critical check and test issues

1 files changed, 47 insertions, 22 deletions

diff --git a/test_dev.log b/test_dev.log
index c57bb958..df159d1e 100644
--- a/test_dev.log
+++ b/test_dev.log
@@ -1,37 +1,62 @@
 Loading mkin
+Loading required package: parallel
 Testing mkin
 ✔ |  OK F W S | Context
-✔ |   4       | AIC calculation
+✔ |   5       | AIC calculation
 ✔ |   2       | Export dataset for reading into CAKE
-✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9 s]
-✔ |   4       | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ |   7       | Fitting the SFORB model [3.1 s]
-✔ |   5       | Analytical solutions for coupled models [2.8 s]
+✔ |  14       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.0 s]
+✔ |   4       | Calculation of FOCUS chi2 error levels [0.5 s]
+✔ |   7       | Fitting the SFORB model [3.4 s]
+✔ |   5       | Analytical solutions for coupled models [3.1 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [0.9 s]
-✔ |  14       | Error model fitting [3.8 s]
+✔ |  14       | Confidence intervals and p-values [1.2 s]
+✔ |  14       | Error model fitting [5.8 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]
-✔ |   1       | Test dataset class mkinds used in gmkin
-✔ |   1       | mkinfit features [0.2 s]
-✔ |  12       | Special cases of mkinfit calls [0.6 s]
+✔ |   5     3 | Nonlinear mixed-effects models [0.1 s]
+────────────────────────────────────────────────────────────────────────────────
+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]
 ✔ |   8       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.3 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [1.3 s]
-✔ |   9       | Nonlinear mixed-effects models [7.3 s]
-✔ |  14       | Plotting [1.3 s]
+✔ |  14     2 | Evaluations according to 2015 NAFTA guidance [2.2 s]
+────────────────────────────────────────────────────────────────────────────────
+Skip (test_nafta.R:25:5): Test data from Appendix B are correctly evaluated
+Reason: getRversion() >= "4.1.0"  is TRUE
+
+Skip (test_nafta.R:53:5): Test data from Appendix D are correctly evaluated
+Reason: getRversion() >= "4.1.0"  is TRUE
+────────────────────────────────────────────────────────────────────────────────
+✔ |   9       | Nonlinear mixed-effects models [7.9 s]
+✔ |   0     1 | Plotting [0.7 s]
+────────────────────────────────────────────────────────────────────────────────
+Skip (test_plot.R:18:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Reason: getRversion() >= "4.1.0"  is TRUE
+────────────────────────────────────────────────────────────────────────────────
 ✔ |   4       | Residuals extracted from mkinfit models
 ✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
-✔ |   4       | Summary
+✔ |   4       | Summary [0.1 s]
 ✔ |   1       | Summaries of old mkinfit objects
-✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.0 s]
-✔ |   9       | Hypothesis tests [7.4 s]
-✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
+✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2 s]
+✔ |   9       | Hypothesis tests [7.7 s]
+✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.0 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 36.9 s
+Duration: 41.2 s
+
+── Skipped tests  ──────────────────────────────────────────────────────────────
+● !saemix_available  is TRUE (3)
+● getRversion() >= "4.1.0"  is TRUE (3)
 
-OK:       162
-Failed:   0
-Warnings: 0
-Skipped:  0
+[ FAIL 0 | WARN 0 | SKIP 6 | PASS 160 ]