diff options
| -rw-r--r-- | test.log | 26 | ||||
| -rw-r--r-- | test_dev.log | 55 |
2 files changed, 27 insertions, 54 deletions
@@ -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 ] |