diff options
| -rw-r--r-- | log/test_dev.log | 65 |
1 files changed, 23 insertions, 42 deletions
diff --git a/log/test_dev.log b/log/test_dev.log index 1612e32d..370dc5af 100644 --- a/log/test_dev.log +++ b/log/test_dev.log @@ -1,35 +1,25 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.3s] +✔ | 5 | Analytical solutions for coupled models [3.0s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [1.1s] -✔ | 1 12 | Dimethenamid data from 2018 [33.8s] +✔ | 12 | Confidence intervals and p-values [1.0s] +✔ | 1 12 | Dimethenamid data from 2018 [31.6s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.7s] +✔ | 14 | Error model fitting [5.2s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] +✔ | 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 [0.4s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] ✔ | 1 | Fitting the logistic model [0.2s] -✖ | 1 9 | Batch fitting and diagnosing hierarchical kinetic models [25.5s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [40.7s] +✖ | 1 1 10 | Nonlinear mixed-effects models [13.2s] ──────────────────────────────────────────────────────────────────────────────── -Failure ('test_mhmkin.R:55'): Multiple hierarchical kinetic models can be fitted and diagnosed -Results have changed from known value recorded in 'illparms_hfits_synth_no_ranef_auto.txt'. - - old | new -[1] " error" | " error" [1] -[2] "degradation const tc " | "degradation const tc " [2] -[3] " SFO sd(parent_0)" | " SFO sd(parent_0)" [3] -[4] " FOMC b.1 " - " FOMC " [4] -──────────────────────────────────────────────────────────────────────────────── -✖ | 1 1 10 | Nonlinear mixed-effects models [13.4s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_mixed.R:20'): Print methods work +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] @@ -50,15 +40,15 @@ old[13:23] vs new[13:23] "SD.log_k1 0.37 0.23 0.51" and 1 more ... -Skip ('test_mixed.R:77'): saemix results are reproducible for biphasic fits +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 [0.5s] -✔ | 3 | mkinfit features [0.8s] +✔ | 10 | Special cases of mkinfit calls [0.6s] +✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✖ | 4 8 | Multistart method for saem.mmkin models [53.5s] +✖ | 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 @@ -68,14 +58,6 @@ Backtrace: at test_multistart.R:44:2 3. testthat::expect_snapshot_file(...) -Failure ('test_multistart.R:49'): multistart works for saem.mmkin models -Snapshot of `testcase` to 'multistart/parplot-for-sfo-fit.svg' has changed -Run `testthat::snapshot_review('multistart/')` to review changes -Backtrace: - 1. vdiffr::expect_doppelganger("parplot for sfo fit", parplot_sfo) - at test_multistart.R:49:2 - 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 @@ -92,9 +74,9 @@ Backtrace: at test_multistart.R:56:2 3. testthat::expect_snapshot_file(...) ──────────────────────────────────────────────────────────────────────────────── -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] -✖ | 1 14 | Plotting [10.5s] +✔ | 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 @@ -105,27 +87,26 @@ Backtrace: 3. testthat::expect_snapshot_file(...) ──────────────────────────────────────────────────────────────────────────────── ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [74.3s] +✔ | 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 [3.9s] +✔ | 10 | Fitting the SFORB model [3.5s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.4s] -✔ | 9 | Hypothesis tests [8.8s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.1s] +✔ | 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: 256.2 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 7 | WARN 0 | SKIP 3 | PASS 263 ] -Error while shutting down parallel: unable to terminate some child processes +[ FAIL 5 | WARN 0 | SKIP 3 | PASS 265 ] |