From 7035cde3a53781721fe15a8893fdf328c789bdd2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 7 Mar 2022 12:03:40 +0100 Subject: Remove nlmixr interface for release of mkin 1.1.0 I am postponing my attempts to get the nlmixr interface to CRAN, given some problems with nlmixr using R-devel under Windows, see https://github.com/nlmixrdevelopment/nlmixr/issues/596 and https://github.com/r-hub/rhub/issues/512, which is fixed by the removal of nlmixr from the testsuite. For the tests to be more platform independent, the biphasic mixed effects models test dataset was defined in a way that fitting should be more robust (less ill-defined). --- test.log | 45 +++++++++++++++++++++------------------------ 1 file changed, 21 insertions(+), 24 deletions(-) (limited to 'test.log') diff --git a/test.log b/test.log index aa74c329..890d921c 100644 --- a/test.log +++ b/test.log @@ -3,52 +3,49 @@ Loading required package: parallel ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [4.2s] +✔ | 5 | Analytical solutions for coupled models [3.3s] ✔ | 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 [63.8s] +✔ | 1 12 | Dimethenamid data from 2018 [31.2s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_dmta.R:164:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [7.0s] +✔ | 14 | Error model fitting [4.7s] ✔ | 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) [1.1s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.5s] -✔ | 1 | Fitting the logistic model [0.3s] -⠇ | 9 | Nonlinear mixed-effects models -✔ | 1 14 | Nonlinear mixed-effects models [1.6s] +✔ | 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 [0.3s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 1 12 | Nonlinear mixed-effects models [0.2s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:68:3): 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] +✔ | 10 | Special cases of mkinfit calls [0.4s] +✔ | 3 | mkinfit features [0.6s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.0s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.1s] -✔ | 16 | Plotting [1.5s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.0s] +✔ | 16 | Plotting [1.3s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 23 | saemix parent models [29.3s] -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s] -✔ | 7 | Fitting the SFORB model [4.6s] +✔ | 23 | saemix parent models [26.7s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] +✔ | 7 | Fitting the SFORB model [3.6s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 4 | Summary [0.1s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s] -✔ | 9 | Hypothesis tests [9.3s] -✔ | 2 | tffm0 +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [8.1s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 145.2 s +Duration: 99.2 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) -[ FAIL 0 | WARN 0 | SKIP 2 | PASS 240 ] +[ FAIL 0 | WARN 0 | SKIP 2 | PASS 221 ] -- cgit v1.2.1