From 75d436be311fff523148dbb078d4c8336740dea5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 3 Mar 2022 10:23:16 +0100 Subject: More work to try to pass tests on R-devel winbuilder --- test_dev.log | 117 ++++++++++++++++++++++++++++++++++------------------------- 1 file changed, 68 insertions(+), 49 deletions(-) (limited to 'test_dev.log') 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 ] -- cgit v1.2.1