From f99bdd8697c3bfbd432a320774a4692fd0e1241a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 6 Jan 2021 20:34:52 +0100 Subject: Make saemix and corresponding tests optional Address release critical check and test issues --- test.log | 52 +++++++++++++++++++++++++++++----------------------- 1 file changed, 29 insertions(+), 23 deletions(-) (limited to 'test.log') diff --git a/test.log b/test.log index 7a9c55ed..ead5a1c7 100644 --- a/test.log +++ b/test.log @@ -4,41 +4,47 @@ 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] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1 s] ✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] -✔ | 7 | Fitting the SFORB model [3.6 s] -✔ | 5 | Analytical solutions for coupled models [3.3 s] +✔ | 7 | Fitting the SFORB model [4.0 s] +✔ | 5 | Analytical solutions for coupled models [3.6 s] ✔ | 5 | Calculation of Akaike weights -✔ | 14 | Confidence intervals and p-values [1.2 s] -✔ | 14 | Error model fitting [5.6 s] +✔ | 14 | Confidence intervals and p-values [1.4 s] +✔ | 14 | Error model fitting [6.8 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] -✔ | 33 1 | Nonlinear mixed effects models [28.7 s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.5 s] +✔ | 1 | Fitting the logistic model [0.3 s] +✔ | 5 3 | Nonlinear mixed-effects models [0.1 s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_mixed.R:143:3): saem results are reproducible for biphasic fits -Reason: Fitting with saemix takes around 10 minutes when using deSolve +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 ──────────────────────────────────────────────────────────────────────────────── ✔ | 2 | Test dataset classes mkinds and mkindsg -✔ | 1 | mkinfit features [0.3 s] -✔ | 10 | Special cases of mkinfit calls [0.3 s] +✔ | 1 | mkinfit features [0.4 s] +✔ | 10 | Special cases of mkinfit calls [0.4 s] ✔ | 8 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.4 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.7 s] -✔ | 9 | Nonlinear mixed-effects models [8.2 s] -✔ | 16 | Plotting [1.9 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.0 s] +✔ | 9 | Nonlinear mixed-effects models [9.3 s] +✔ | 14 | Plotting [2.0 s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6 s] -✔ | 4 | Summary [0.1 s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.8 s] +✔ | 4 | Summary [0.2 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s] -✔ | 9 | Hypothesis tests [7.3 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5 s] +✔ | 9 | Hypothesis tests [7.9 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.7 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 71.3 s +Duration: 48.3 s ── Skipped tests ────────────────────────────────────────────────────────────── -● Fitting with saemix takes around 10 minutes when using deSolve (1) +● !saemix_available is TRUE (3) -[ FAIL 0 | WARN 0 | SKIP 1 | PASS 206 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 176 ] -- cgit v1.2.1