R-devel with openblas

2 files changed, 27 insertions, 54 deletions

diff --git a/test.log b/test.log
index c2dac1d7..aa74c329 100644
--- a/test.log
+++ b/test.log
@@ -3,24 +3,24 @@ Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [4.3s]
+✔ |         5 | Analytical solutions for coupled models [4.2s]
 ✔ |         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 [62.6s]
+✔ |     1  27 | Dimethenamid data from 2018 [63.8s]
 ────────────────────────────────────────────────────────────────────────────────
 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
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [6.9s]
+✔ |        14 | Error model fitting [7.0s]
 ✔ |         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) [1.1s]
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.5s]
 ✔ |         1 | Fitting the logistic model [0.3s]
-⠴ |         6 | Nonlinear mixed-effects models                                  
-✔ |     1  14 | Nonlinear mixed-effects models [1.3s]
+⠇ |         9 | Nonlinear mixed-effects models                                  
+✔ |     1  14 | Nonlinear mixed-effects models [1.6s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
@@ -30,22 +30,22 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         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 [9.4s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.0s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [9.1s]
 ✔ |        16 | Plotting [1.5s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        23 | saemix parent models [29.4s]
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.7s]
-✔ |         7 | Fitting the SFORB model [4.4s]
+✔ |        23 | saemix parent models [29.3s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s]
+✔ |         7 | Fitting the SFORB model [4.6s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         4 | Summary [0.1s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.6s]
-✔ |         9 | Hypothesis tests [9.4s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s]
+✔ |         9 | Hypothesis tests [9.3s]
 ✔ |         2 | tffm0
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 144.3 s
+Duration: 145.2 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/test_dev.log b/test_dev.log
index 041804e9..24905a1a 100644
--- a/test_dev.log
+++ b/test_dev.log
@@ -3,35 +3,25 @@ Loading required package: parallel
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [14.4s]
+✔ |         5 | Analytical solutions for coupled models [14.6s]
 ✔ |         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]
+✔ |     1  27 | Dimethenamid data from 2018 [116.1s]
 ────────────────────────────────────────────────────────────────────────────────
 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
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [6.8s]
+✔ |        14 | Error model fitting [6.6s]
 ✔ |         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]
+⠋ |        11 | Nonlinear mixed-effects models                                  
+✔ |     1  14 | Nonlinear mixed-effects models [1.3s]
 ────────────────────────────────────────────────────────────────────────────────
-Failure (test_mixed.R:5:3): Print methods work
-Results have changed from known value recorded in 'print_mmkin_dfop_1_mixed.txt'.
-
-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
 ────────────────────────────────────────────────────────────────────────────────
@@ -41,41 +31,24 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ✔ |         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]
-────────────────────────────────────────────────────────────────────────────────
-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(...)
-────────────────────────────────────────────────────────────────────────────────
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.7s]
+✔ |        16 | Plotting [1.4s]
 ✔ |         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]
+✔ |        23 | saemix parent models [28.4s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [12.0s]
+✔ |         7 | Fitting the SFORB model [16.9s]
 ✔ |         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]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [18.1s]
+✔ |         9 | Hypothesis tests [78.9s]
 ✔ |         2 | tffm0
 ✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 314.2 s
+Duration: 315.9 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • 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 3 | WARN 0 | SKIP 2 | PASS 237 ]
+[ FAIL 0 | WARN 0 | SKIP 2 | PASS 240 ]