diff options
Diffstat (limited to 'log/test_dev.log')
| -rw-r--r-- | log/test_dev.log | 116 |
1 files changed, 87 insertions, 29 deletions
diff --git a/log/test_dev.log b/log/test_dev.log index 24905a1a..370dc5af 100644 --- a/log/test_dev.log +++ b/log/test_dev.log @@ -1,54 +1,112 @@ -ℹ Loading mkin -Loading required package: parallel ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [14.6s] +✔ | 5 | Analytical solutions for coupled models [3.0s] ✔ | 5 | Calculation of Akaike weights -✔ | 2 | Export dataset for reading into CAKE +✔ | 3 | 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 [116.1s] +✔ | 1 12 | Dimethenamid data from 2018 [31.6s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Skip ('test_dmta.R:98'): 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 [6.6s] +✔ | 14 | Error model fitting [5.2s] ✔ | 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] -⠋ | 11 | Nonlinear mixed-effects models -✔ | 1 14 | Nonlinear mixed-effects models [1.3s] -──────────────────────────────────────────────────────────────────────────────── -Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits +✔ | 4 | Calculation of FOCUS chi2 error levels [0.5s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [40.7s] +✖ | 1 1 10 | Nonlinear mixed-effects models [13.2s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_mixed.R:21'): 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:78'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls [0.6s] -✔ | 3 | mkinfit features [1.1s] +✔ | 3 | mkinfit features [0.7s] ✔ | 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 [8.7s] -✔ | 16 | Plotting [1.4s] +✖ | 3 9 | Multistart method for saem.mmkin models [45.8s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_multistart.R:44'): 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'): 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'): 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 [2.3s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.0s] +✖ | 1 14 | Plotting [10.2s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_plot.R:55'): 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 -✔ | 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 36 | saemix parent models [71.7s] +──────────────────────────────────────────────────────────────────────────────── +Skip ('test_saemix_parent.R:143'): 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 [1.5s] +✔ | 11 | Processing of residue series +✔ | 10 | Fitting the SFORB model [3.5s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Summary [0.1s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [18.1s] -✔ | 9 | Hypothesis tests [78.9s] -✔ | 2 | tffm0 +✔ | 5 | Summary [0.2s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [7.7s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 315.9 s +Duration: 255.0 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) +• This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 2 | PASS 240 ] +[ FAIL 5 | WARN 0 | SKIP 3 | PASS 265 ] |