More work to try to pass tests on R-devel winbuilder

1 files changed, 68 insertions, 49 deletions

diff --git a/test_dev.log b/test_dev.log
index df159d1e..041804e9 100644
--- a/test_dev.log
+++ b/test_dev.log
@@ -1,62 +1,81 @@
-Loading mkin
+ℹ Loading mkin
 Loading required package: parallel
-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]
-✔ |   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
-✔ |  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]
-✔ |   5     3 | Nonlinear mixed-effects models [0.1 s]
+ℹ Testing mkin
+✔ | F W S  OK | Context
+✔ |         5 | AIC calculation
+✔ |         5 | Analytical solutions for coupled models [14.4s]
+✔ |         5 | Calculation of Akaike weights
+✔ |         2 | Export dataset for reading into CAKE
+✔ |        12 | Confidence intervals and p-values [1.0s]
+⠋ |         1 | Dimethenamid data from 2018                                     
+✔ |     1  27 | Dimethenamid data from 2018 [124.8s]
 ────────────────────────────────────────────────────────────────────────────────
-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
+Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |   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]
-✔ |  14     2 | Evaluations according to 2015 NAFTA guidance [2.2 s]
+✔ |        14 | Error model fitting [6.8s]
+✔ |         5 | Time step normalisation
+✔ |         4 | Calculation of FOCUS chi2 error levels [0.8s]
+✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.6s]
+✔ |         1 | Fitting the logistic model [0.3s]
+⠇ | 1       8 | Nonlinear mixed-effects models                                  
+✖ | 1   1  13 | Nonlinear mixed-effects models [1.5s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_nafta.R:25:5): Test data from Appendix B are correctly evaluated
-Reason: getRversion() >= "4.1.0"  is TRUE
+Failure (test_mixed.R:5:3): Print methods work
+Results have changed from known value recorded in 'print_mmkin_dfop_1_mixed.txt'.
 
-Skip (test_nafta.R:53:5): Test data from Appendix D are correctly evaluated
-Reason: getRversion() >= "4.1.0"  is TRUE
+old[18:21] vs new[18:21]
+  ""
+  "Mean fitted parameters:"
+  "parent_0   log_k1   log_k2 g_qlogis "
+- "  100.06    -2.68    -5.57     0.01 "
++ "  100.06    -2.68    -5.58     0.01 "
+
+Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
+Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
-✔ |   9       | Nonlinear mixed-effects models [7.9 s]
-✔ |   0     1 | Plotting [0.7 s]
+✔ |         3 | Test dataset classes mkinds and mkindsg
+✔ |        10 | Special cases of mkinfit calls [0.6s]
+✔ |         3 | mkinfit features [1.1s]
+✔ |         8 | mkinmod model generation and printing [0.2s]
+✔ |         3 | Model predictions with mkinpredict [0.3s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.1s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.5s]
+✖ | 2      14 | Plotting [1.5s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip (test_plot.R:18:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
-Reason: getRversion() >= "4.1.0"  is TRUE
+Failure (test_plot.R:42:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Snapshot of `testcase` to 'plot/mixed-model-fit-for-nlme-object.svg' has changed
+Run `testthat::snapshot_review('plot/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger(...)
+      at test_plot.R:42:2
+ 3. testthat::expect_snapshot_file(...)
+
+Failure (test_plot.R:50:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Snapshot of `testcase` to 'plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed
+Run `testthat::snapshot_review('plot/')` to review changes
+Backtrace:
+ 1. vdiffr::expect_doppelganger(...)
+      at test_plot.R:50:2
+ 3. testthat::expect_snapshot_file(...)
 ────────────────────────────────────────────────────────────────────────────────
-✔ |   4       | Residuals extracted from mkinfit models
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
-✔ |   4       | Summary [0.1 s]
-✔ |   1       | Summaries of old mkinfit objects
-✔ |   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]
+✔ |         4 | Residuals extracted from mkinfit models
+✔ |        23 | saemix_parent [28.7s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.2s]
+✔ |         7 | Fitting the SFORB model [16.1s]
+✔ |         1 | Summaries of old mkinfit objects
+✔ |         4 | Summary [0.1s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [19.0s]
+✔ |         9 | Hypothesis tests [67.6s]
+✔ |         2 | tffm0
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 41.2 s
+Duration: 314.2 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
-● !saemix_available  is TRUE (3)
-● getRversion() >= "4.1.0"  is TRUE (3)
+• Fitting this ODE model with saemix takes about 15 minutes on my system (1)
+• Fitting with saemix takes around 10 minutes when using deSolve (1)
 
-[ FAIL 0 | WARN 0 | SKIP 6 | PASS 160 ]
+[ FAIL 3 | WARN 0 | SKIP 2 | PASS 237 ]