ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation ✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] ✔ | 12 | Confidence intervals and p-values [0.4s] ✔ | 1 12 | Dimethenamid data from 2018 [13.2s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system ──────────────────────────────────────────────────────────────────────────────── ✔ | 14 | Error model fitting [2.5s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.3s] ✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.4s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2s] ✔ | 1 | Fitting the logistic model [0.1s] ✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s] ✖ | 1 2 15 | Nonlinear mixed-effects models [149.2s] ──────────────────────────────────────────────────────────────────────────────── Failure ('test_mixed.R:21:3'): Print methods work Results have changed from known value recorded in 'print_dfop_saem_1.txt'. old[13:23] vs new[13:23] "" "Fitted parameters:" " estimate lower upper" - "parent_0 99.92 98.77 101.06" + "parent_0 99.96 98.82 101.11" - "log_k1 -2.72 -2.95 -2.50" + "log_k1 -2.71 -2.94 -2.49" - "log_k2 -4.14 -4.27 -4.01" + "log_k2 -4.14 -4.26 -4.01" - "g_qlogis -0.35 -0.53 -0.16" + "g_qlogis -0.36 -0.54 -0.17" - "a.1 0.92 0.68 1.16" + "a.1 0.93 0.69 1.17" "b.1 0.05 0.04 0.06" "SD.log_k1 0.37 0.23 0.51" and 1 more ... Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work Reason: This is seldom used, so save some time ──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls [0.3s] ✔ | 3 | mkinfit features [0.5s] ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict [0.1s] ✖ | 3 9 | Multistart method for saem.mmkin models [23.2s] ──────────────────────────────────────────────────────────────────────────────── Failure ('test_multistart.R:44:3'): multistart works for saem.mmkin models Snapshot of `testcase` to 'multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.svg' has changed Run `testthat::snapshot_review('multistart/')` to review changes Backtrace: 1. vdiffr::expect_doppelganger(...) at test_multistart.R:44:2 3. testthat::expect_snapshot_file(...) Failure ('test_multistart.R:55:3'): multistart works for saem.mmkin models Snapshot of `testcase` to 'multistart/llhist-for-dfop-sfo-fit.svg' has changed Run `testthat::snapshot_review('multistart/')` to review changes Backtrace: 1. vdiffr::expect_doppelganger("llhist for dfop sfo fit", llhist_dfop_sfo) at test_multistart.R:55:2 3. testthat::expect_snapshot_file(...) Failure ('test_multistart.R:56:3'): multistart works for saem.mmkin models Snapshot of `testcase` to 'multistart/parplot-for-dfop-sfo-fit.svg' has changed Run `testthat::snapshot_review('multistart/')` to review changes Backtrace: 1. vdiffr::expect_doppelganger("parplot for dfop sfo fit", parplot_dfop_sfo) at test_multistart.R:56:2 3. testthat::expect_snapshot_file(...) ──────────────────────────────────────────────────────────────────────────────── ✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] ✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] ✖ | 1 14 | Plotting [4.7s] ──────────────────────────────────────────────────────────────────────────────── Failure ('test_plot.R:55:3'): 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:55:2 3. testthat::expect_snapshot_file(...) ──────────────────────────────────────────────────────────────────────────────── ✔ | 4 | Residuals extracted from mkinfit models ✔ | 1 36 | saemix parent models [31.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143:3'): We can also use mkin solution methods for saem Reason: This still takes almost 2.5 minutes although we do not solve ODEs ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s] ✔ | 11 | Processing of residue series ✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] ✔ | 9 | Hypothesis tests [2.9s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ Duration: 262.6 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system (1) • Fitting with saemix takes around 10 minutes when using deSolve (1) • This is seldom used, so save some time (1) • This still takes almost 2.5 minutes although we do not solve ODEs (1) [ FAIL 5 | WARN 0 | SKIP 4 | PASS 276 ]