From 5889cd78376e244f38e6c5acba8ffbc46e18f803 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 16 Nov 2022 13:50:54 +0100 Subject: Address platform dependence that surfaced on winbuilder --- log/test.log | 46 +++++++++++++++++++++++----------------------- 1 file changed, 23 insertions(+), 23 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 7005ac37..eb8d6b9a 100644 --- a/log/test.log +++ b/log/test.log @@ -1,57 +1,57 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.2s] +✔ | 5 | Analytical solutions for coupled models [3.7s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [32.4s] +✔ | 12 | Confidence intervals and p-values [1.1s] +✔ | 1 12 | Dimethenamid data from 2018 [37.5s] ──────────────────────────────────────────────────────────────────────────────── 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 [4.9s] +✔ | 14 | Error model fitting [5.5s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 4 | Calculation of FOCUS chi2 error levels [0.7s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] -✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.2s] -✔ | 1 12 | Nonlinear mixed-effects models [0.3s] +✔ | 1 | Fitting the logistic model [0.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [27.2s] +✔ | 1 12 | Nonlinear mixed-effects models [0.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:74'): 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 [0.7s] +✔ | 10 | Special cases of mkinfit calls [0.6s] +✔ | 3 | mkinfit features [0.8s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 7 | Multistart method for saem.mmkin models [36.9s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.6s] -✔ | 16 | Plotting [9.8s] +✔ | 9 | Multistart method for saem.mmkin models [45.7s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.7s] +✔ | 9 | Nonlinear mixed-effects models with nlme [10.3s] +✔ | 16 | Plotting [11.4s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [66.3s] +✔ | 1 36 | saemix parent models [75.4s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.7s] +✔ | 10 | Fitting the SFORB model [4.2s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.0s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s] +✔ | 9 | Hypothesis tests [9.6s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 211.7 s +Duration: 245.9 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 3 | PASS 267 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 269 ] -- cgit v1.2.1 From 78d421dc463dbfb993e372073c8de406d1f45da7 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 16 Nov 2022 14:51:17 +0100 Subject: Update DESCRIPTION and NEWS, check and test --- log/test.log | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index eb8d6b9a..b305bf58 100644 --- a/log/test.log +++ b/log/test.log @@ -1,22 +1,22 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.7s] +✔ | 5 | Analytical solutions for coupled models [3.5s] ✔ | 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 [37.5s] +✔ | 1 12 | Dimethenamid data from 2018 [34.5s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.5s] +✔ | 14 | Error model fitting [5.3s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.7s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s] +✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] +✔ | 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] -✔ | 1 | Fitting the logistic model [0.3s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [27.2s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.6s] ✔ | 1 12 | Nonlinear mixed-effects models [0.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits @@ -24,30 +24,30 @@ 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 [0.8s] +✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 9 | Multistart method for saem.mmkin models [45.7s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.7s] -✔ | 9 | Nonlinear mixed-effects models with nlme [10.3s] -✔ | 16 | Plotting [11.4s] +✔ | 9 | Multistart method for saem.mmkin models [40.2s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.5s] +✔ | 16 | Plotting [10.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [75.4s] +✔ | 1 36 | saemix parent models [69.8s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.6s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [4.2s] +✔ | 10 | Fitting the SFORB model [3.9s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s] -✔ | 9 | Hypothesis tests [9.6s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +✔ | 9 | Hypothesis tests [8.5s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 245.9 s +Duration: 225.9 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) -- cgit v1.2.1 From df0cff4b829f1abf62f037591a24a8019174dd0a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 08:37:40 +0100 Subject: Pass error.init to saemix_model, show in parplot Due to an oversight, error.init was not really passed to saemix_model in saem.mmkin. The new initial values were reverted to c(1, 1), in order to avoid changing the test results. Initial values for error model parameters are now shown in parplot.multistart. --- log/test.log | 38 +++++++++++++++++++------------------- 1 file changed, 19 insertions(+), 19 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index b305bf58..af8e52fd 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.5s] +✔ | 5 | Analytical solutions for coupled models [3.2s] ✔ | 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 [34.5s] +✔ | 12 | Confidence intervals and p-values [1.0s] +✔ | 1 12 | Dimethenamid data from 2018 [31.4s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.3s] +✔ | 14 | Error model fitting [4.9s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 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] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.6s] -✔ | 1 12 | Nonlinear mixed-effects models [0.4s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [23.9s] +✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:74'): 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] +✔ | 10 | Special cases of mkinfit calls [0.5s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 9 | Multistart method for saem.mmkin models [40.2s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.6s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.5s] -✔ | 16 | Plotting [10.5s] +✔ | 3 | Model predictions with mkinpredict [0.4s] +✔ | 9 | Multistart method for saem.mmkin models [37.0s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] +✔ | 16 | Plotting [10.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [69.8s] +✔ | 1 36 | saemix parent models [66.0s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.6s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.9s] +✔ | 10 | Fitting the SFORB model [3.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] -✔ | 9 | Hypothesis tests [8.5s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [8.0s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 225.9 s +Duration: 211.3 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) -- cgit v1.2.1 From a14237fc1580b09f8772cd3330b0a445785e48ac Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 10:09:28 +0100 Subject: Round parameters with signif() before printing This will hopefully make the test pass on all relevant platforms. --- log/test.log | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index af8e52fd..87d24690 100644 --- a/log/test.log +++ b/log/test.log @@ -1,38 +1,38 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.2s] +✔ | 5 | Analytical solutions for coupled models [3.3s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [31.4s] +✔ | 1 12 | Dimethenamid data from 2018 [31.5s] ──────────────────────────────────────────────────────────────────────────────── 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 [4.9s] +✔ | 14 | Error model fitting [5.0s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 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] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [23.9s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.4s] ✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── -Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits +Skip ('test_mixed.R:79'): 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 [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.4s] -✔ | 9 | Multistart method for saem.mmkin models [37.0s] +✔ | 3 | Model predictions with mkinpredict [0.3s] +✔ | 9 | Multistart method for saem.mmkin models [36.2s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] ✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] -✔ | 16 | Plotting [10.1s] +✔ | 16 | Plotting [10.0s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [66.0s] +✔ | 1 36 | saemix parent models [65.8s] ──────────────────────────────────────────────────────────────────────────────── 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 @@ -47,7 +47,7 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 211.3 s +Duration: 210.4 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) -- cgit v1.2.1 From 5364f037a72863ef5ba81e14ba4417f68fd389f9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 19:14:47 +0100 Subject: Make mixed model test data permanent to ensure reproducibility To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package. --- log/test.log | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 87d24690..d1de270e 100644 --- a/log/test.log +++ b/log/test.log @@ -5,19 +5,19 @@ ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [31.5s] +✔ | 1 12 | Dimethenamid data from 2018 [32.6s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.0s] +✔ | 14 | Error model fitting [5.1s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 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] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.4s] -✔ | 1 12 | Nonlinear mixed-effects models [0.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.6s] +✔ | 1 13 | Nonlinear mixed-effects models [0.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:79'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -26,32 +26,32 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 10 | Special cases of mkinfit calls [0.5s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 9 | Multistart method for saem.mmkin models [36.2s] +✔ | 3 | Model predictions with mkinpredict [0.4s] +✔ | 9 | Multistart method for saem.mmkin models [37.3s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] -✔ | 16 | Plotting [10.0s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] +✔ | 16 | Plotting [10.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [65.8s] +✔ | 1 36 | saemix parent models [71.4s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.4s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.7s] +✔ | 10 | Fitting the SFORB model [3.9s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.0s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +✔ | 9 | Hypothesis tests [8.3s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 210.4 s +Duration: 220.0 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 3 | PASS 269 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ] -- cgit v1.2.1 From b6b7e387261e5483f1bdfafaaa975e2f24c6567c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 20:35:06 +0100 Subject: Use cluster with two cores to reduce windows check time --- log/test.log | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index d1de270e..8fdaec48 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ 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 [3.4s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [1.0s] -✔ | 1 12 | Dimethenamid data from 2018 [32.6s] +✔ | 12 | Confidence intervals and p-values [1.2s] +✔ | 1 12 | Dimethenamid data from 2018 [34.0s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.1s] +✔ | 14 | Error model fitting [5.4s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s] ✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] -✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [24.6s] +✔ | 1 | Fitting the logistic model [0.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.8s] ✔ | 1 13 | Nonlinear mixed-effects models [0.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:79'): 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] +✔ | 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 [0.4s] -✔ | 9 | Multistart method for saem.mmkin models [37.3s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] +✔ | 9 | Multistart method for saem.mmkin models [38.2s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.4s] ✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] -✔ | 16 | Plotting [10.1s] +✔ | 16 | Plotting [10.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [71.4s] +✔ | 1 36 | saemix parent models [75.0s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.6s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.9s] +✔ | 10 | Fitting the SFORB model [4.0s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] -✔ | 9 | Hypothesis tests [8.3s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s] +✔ | 9 | Hypothesis tests [9.0s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 220.0 s +Duration: 229.5 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) @@ -55,3 +55,4 @@ Duration: 220.0 s • This still takes almost 2.5 minutes although we do not solve ODEs (1) [ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ] +Error while shutting down parallel: unable to terminate some child processes -- cgit v1.2.1 From 5ec8e1bad1aa7d79ee9c19bdd50be07f81a14278 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 22:11:02 +0100 Subject: Move two saem fits from setup script to skipped tests Save winbuilder/CRAN check time... --- log/test.log | 44 ++++++++++++++++++++++---------------------- 1 file changed, 22 insertions(+), 22 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 8fdaec48..897bf896 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.4s] +✔ | 5 | Analytical solutions for coupled models [3.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [1.2s] -✔ | 1 12 | Dimethenamid data from 2018 [34.0s] +✔ | 1 12 | Dimethenamid data from 2018 [33.2s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.4s] +✔ | 14 | Error model fitting [5.0s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.9s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] -✔ | 1 | Fitting the logistic model [0.3s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.8s] -✔ | 1 13 | Nonlinear mixed-effects models [0.4s] +✔ | 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 [24.7s] +✔ | 1 11 | Nonlinear mixed-effects models [13.1s] ──────────────────────────────────────────────────────────────────────────────── -Skip ('test_mixed.R:79'): saemix results are reproducible for biphasic fits +Skip ('test_mixed.R:77'): 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] +✔ | 10 | Special cases of mkinfit calls [0.4s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.4s] -✔ | 9 | Multistart method for saem.mmkin models [38.2s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.4s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] -✔ | 16 | Plotting [10.5s] +✔ | 3 | Model predictions with mkinpredict [0.3s] +✔ | 12 | Multistart method for saem.mmkin models [49.5s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] +✔ | 15 | Plotting [10.3s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [75.0s] +✔ | 1 36 | saemix parent models [72.5s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.6s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [4.0s] +✔ | 10 | Fitting the SFORB model [3.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.5s] -✔ | 9 | Hypothesis tests [9.0s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [8.2s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 229.5 s +Duration: 246.1 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) -- cgit v1.2.1 From 64e245a16ec22cf864fcb5bae3b4b2fb2eee5905 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 19 Nov 2022 00:17:33 +0100 Subject: Confirm which test fail on R-devel --- log/test.log | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 897bf896..0b9aa7eb 100644 --- a/log/test.log +++ b/log/test.log @@ -1,11 +1,11 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.5s] +✔ | 5 | Analytical solutions for coupled models [3.3s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [1.2s] -✔ | 1 12 | Dimethenamid data from 2018 [33.2s] +✔ | 12 | Confidence intervals and p-values [1.1s] +✔ | 1 12 | Dimethenamid data from 2018 [33.3s] ──────────────────────────────────────────────────────────────────────────────── 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 @@ -14,40 +14,40 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 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 [24.7s] -✔ | 1 11 | Nonlinear mixed-effects models [13.1s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] +✔ | 1 | Fitting the logistic model [0.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.5s] +✔ | 1 11 | Nonlinear mixed-effects models [13.2s] ──────────────────────────────────────────────────────────────────────────────── -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 [0.4s] +✔ | 10 | Special cases of mkinfit calls [0.5s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 12 | Multistart method for saem.mmkin models [49.5s] +✔ | 12 | Multistart method for saem.mmkin models [51.1s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.8s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] ✔ | 15 | Plotting [10.3s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [72.5s] +✔ | 1 36 | saemix parent models [73.7s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] ✔ | 11 | Processing of residue series ✔ | 10 | Fitting the SFORB model [3.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.2s] +✔ | 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) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 246.1 s +Duration: 251.2 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) -- cgit v1.2.1 From aaa4cab7e0c7212f91147a9789af54b97fe342ca Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 29 Nov 2022 20:23:17 +0100 Subject: Complete starting values in summary for saem.mmkin fits Also update tests to the changes in mhmkin (see NEWS) --- log/test.log | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 0b9aa7eb..e17ecc1f 100644 --- a/log/test.log +++ b/log/test.log @@ -5,54 +5,54 @@ ✔ | 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 [33.3s] +✔ | 1 12 | Dimethenamid data from 2018 [32.2s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.0s] +✔ | 14 | Error model fitting [4.9s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 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] -✔ | 1 | Fitting the logistic model [0.3s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [25.5s] -✔ | 1 11 | Nonlinear mixed-effects models [13.2s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 8 | Batch fitting and diagnosing hierarchical kinetic models [14.5s] +✔ | 1 11 | Nonlinear mixed-effects models [13.1s] ──────────────────────────────────────────────────────────────────────────────── 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] +✔ | 10 | Special cases of mkinfit calls [0.4s] ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 12 | Multistart method for saem.mmkin models [51.1s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] -✔ | 15 | Plotting [10.3s] +✔ | 12 | Multistart method for saem.mmkin models [50.1s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s] +✔ | 15 | Plotting [10.2s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [73.7s] +✔ | 1 36 | saemix parent models [103.8s] ──────────────────────────────────────────────────────────────────────────────── 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] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series ✔ | 10 | Fitting the SFORB model [3.8s] ✔ | 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 | 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: 251.2 s +Duration: 266.0 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 3 | PASS 270 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 268 ] Error while shutting down parallel: unable to terminate some child processes -- cgit v1.2.1 From 74e44dfed5af6e6fd421abe82d3e3f190771f85a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 1 Dec 2022 11:20:00 +0100 Subject: Possibility to manually specify no_random_effects in mhmkin --- log/test.log | 48 ++++++++++++++++++++++++------------------------ 1 file changed, 24 insertions(+), 24 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index e17ecc1f..84fa49b9 100644 --- a/log/test.log +++ b/log/test.log @@ -1,58 +1,58 @@ 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 [4.2s] ✔ | 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 [32.2s] +✔ | 12 | Confidence intervals and p-values [1.2s] +✔ | 1 12 | Dimethenamid data from 2018 [42.0s] ──────────────────────────────────────────────────────────────────────────────── 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 [4.9s] +✔ | 14 | Error model fitting [6.5s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] -✔ | 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] -✔ | 8 | Batch fitting and diagnosing hierarchical kinetic models [14.5s] -✔ | 1 11 | Nonlinear mixed-effects models [13.1s] +✔ | 4 | Calculation of FOCUS chi2 error levels [0.7s] +✔ | 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] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [54.1s] +✔ | 1 11 | Nonlinear mixed-effects models [14.3s] ──────────────────────────────────────────────────────────────────────────────── 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 [0.4s] -✔ | 3 | mkinfit features [0.7s] -✔ | 8 | mkinmod model generation and printing [0.2s] +✔ | 10 | Special cases of mkinfit calls [0.8s] +✔ | 3 | mkinfit features [0.9s] +✔ | 8 | mkinmod model generation and printing [0.3s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 12 | Multistart method for saem.mmkin models [50.1s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s] -✔ | 15 | Plotting [10.2s] +✔ | 12 | Multistart method for saem.mmkin models [80.1s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.8s] +✔ | 9 | Nonlinear mixed-effects models with nlme [11.4s] +✔ | 15 | Plotting [12.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [103.8s] +✔ | 1 36 | saemix parent models [85.9s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.9s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.8s] +✔ | 10 | Fitting the SFORB model [4.6s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.1s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.9s] +✔ | 9 | Hypothesis tests [11.0s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 266.0 s +Duration: 342.6 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 3 | PASS 268 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ] Error while shutting down parallel: unable to terminate some child processes -- cgit v1.2.1 From 240568bf65f2257f1185927ac811dde18aeabe1d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 2 Dec 2022 13:25:56 +0100 Subject: Avoid error message at testthat termination https://github.com/r-lib/processx/issues/236 --- log/test.log | 47 +++++++++++++++++++++++------------------------ 1 file changed, 23 insertions(+), 24 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 84fa49b9..5764f209 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ 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 ✔ | 3 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [1.2s] -✔ | 1 12 | Dimethenamid data from 2018 [42.0s] +✔ | 12 | Confidence intervals and p-values [1.1s] +✔ | 1 12 | Dimethenamid data from 2018 [31.9s] ──────────────────────────────────────────────────────────────────────────────── 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 [6.5s] +✔ | 14 | Error model fitting [4.9s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.7s] -✔ | 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] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [54.1s] -✔ | 1 11 | Nonlinear mixed-effects models [14.3s] +✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] +✔ | 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 [41.4s] +✔ | 1 11 | Nonlinear mixed-effects models [13.3s] ──────────────────────────────────────────────────────────────────────────────── 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 [0.8s] -✔ | 3 | mkinfit features [0.9s] -✔ | 8 | mkinmod model generation and printing [0.3s] +✔ | 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] -✔ | 12 | Multistart method for saem.mmkin models [80.1s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.8s] -✔ | 9 | Nonlinear mixed-effects models with nlme [11.4s] -✔ | 15 | Plotting [12.1s] +✔ | 12 | Multistart method for saem.mmkin models [47.5s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.5s] +✔ | 15 | Plotting [10.2s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [85.9s] +✔ | 1 36 | saemix parent models [73.0s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.9s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [4.6s] +✔ | 10 | Fitting the SFORB model [3.9s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.9s] -✔ | 9 | Hypothesis tests [11.0s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [8.4s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 342.6 s +Duration: 261.1 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) @@ -55,4 +55,3 @@ Duration: 342.6 s • This still takes almost 2.5 minutes although we do not solve ODEs (1) [ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ] -Error while shutting down parallel: unable to terminate some child processes -- cgit v1.2.1 From 478c6d5eec4c84b22b43adcbdf36888b302ead00 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 6 Dec 2022 10:33:24 +0100 Subject: Some parplot improvements llquant argument, improved legend text, tests --- log/test.log | 41 +++++++++++++++++++++++++---------------- 1 file changed, 25 insertions(+), 16 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 5764f209..7614b136 100644 --- a/log/test.log +++ b/log/test.log @@ -1,22 +1,22 @@ 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 [3.2s] ✔ | 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 [31.9s] +✔ | 1 12 | Dimethenamid data from 2018 [32.0s] ──────────────────────────────────────────────────────────────────────────────── 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 [4.9s] +✔ | 14 | Error model fitting [4.8s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 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 [41.4s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [42.2s] ✔ | 1 11 | Nonlinear mixed-effects models [13.3s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits @@ -26,32 +26,41 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 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] -✔ | 12 | Multistart method for saem.mmkin models [47.5s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.3s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.5s] -✔ | 15 | Plotting [10.2s] +✔ | 3 | Model predictions with mkinpredict [0.4s] +✖ | 1 11 | Multistart method for saem.mmkin models [46.7s] +──────────────────────────────────────────────────────────────────────────────── +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 [2.2s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.4s] +✔ | 15 | Plotting [10.1s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [73.0s] +✔ | 1 36 | saemix parent models [73.6s] ──────────────────────────────────────────────────────────────────────────────── 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] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.9s] +✔ | 10 | Fitting the SFORB model [3.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.4s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +✔ | 9 | Hypothesis tests [8.1s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 261.1 s +Duration: 260.9 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 3 | PASS 270 ] +[ FAIL 1 | WARN 0 | SKIP 3 | PASS 269 ] -- cgit v1.2.1 From 97f71fc3d086bd447ab3e4d19abf32bb3114085b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 7 Dec 2022 14:41:52 +0100 Subject: Check slopes in saemix covariate models --- log/test.log | 41 ++++++++++++++++------------------------- 1 file changed, 16 insertions(+), 25 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 7614b136..af2ffc41 100644 --- a/log/test.log +++ b/log/test.log @@ -1,23 +1,23 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.2s] +✔ | 5 | Analytical solutions for coupled models [3.4s] ✔ | 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 [32.0s] +✔ | 1 12 | Dimethenamid data from 2018 [32.7s] ──────────────────────────────────────────────────────────────────────────────── 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 [4.8s] +✔ | 14 | Error model fitting [5.0s] ✔ | 5 | Time step normalisation ✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] ✔ | 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] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.4s] ✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [42.2s] -✔ | 1 11 | Nonlinear mixed-effects models [13.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [43.4s] +✔ | 1 11 | Nonlinear mixed-effects models [13.5s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -27,40 +27,31 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve ✔ | 3 | mkinfit features [0.7s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.4s] -✖ | 1 11 | Multistart method for saem.mmkin models [46.7s] -──────────────────────────────────────────────────────────────────────────────── -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(...) -──────────────────────────────────────────────────────────────────────────────── +✔ | 12 | Multistart method for saem.mmkin models [50.1s] ✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.4s] -✔ | 15 | Plotting [10.1s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.8s] +✔ | 15 | Plotting [10.5s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [73.6s] +✔ | 1 36 | saemix parent models [85.7s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.4s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.7s] +✔ | 10 | Fitting the SFORB model [3.9s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] -✔ | 9 | Hypothesis tests [8.1s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] +✔ | 9 | Hypothesis tests [8.2s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 260.9 s +Duration: 280.1 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 1 | WARN 0 | SKIP 3 | PASS 269 ] +[ FAIL 0 | WARN 0 | SKIP 3 | PASS 270 ] -- cgit v1.2.1 From 7c8b3db180be371cb03b9518f14117060fbc4239 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 12 Dec 2022 12:20:50 +0100 Subject: Run tests with new CPU and RAM --- log/test.log | 52 ++++++++++++++++++++++++++-------------------------- 1 file changed, 26 insertions(+), 26 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index af2ffc41..89265100 100644 --- a/log/test.log +++ b/log/test.log @@ -1,53 +1,53 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.4s] +✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 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 [32.7s] +✔ | 12 | Confidence intervals and p-values [0.4s] +✔ | 1 12 | Dimethenamid data from 2018 [12.3s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.0s] +✔ | 14 | Error model fitting [2.3s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] -✔ | 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] -✔ | 1 | Fitting the logistic model [0.2s] -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [43.4s] -✔ | 1 11 | Nonlinear mixed-effects models [13.5s] +✔ | 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 [18.2s] +✔ | 1 11 | Nonlinear mixed-effects models [5.8s] ──────────────────────────────────────────────────────────────────────────────── 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 [0.7s] -✔ | 8 | mkinmod model generation and printing [0.2s] -✔ | 3 | Model predictions with mkinpredict [0.4s] -✔ | 12 | Multistart method for saem.mmkin models [50.1s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.2s] -✔ | 9 | Nonlinear mixed-effects models with nlme [9.8s] -✔ | 15 | Plotting [10.5s] +✔ | 10 | Special cases of mkinfit calls [0.4s] +✔ | 3 | mkinfit features [0.4s] +✔ | 8 | mkinmod model generation and printing +✔ | 3 | Model predictions with mkinpredict [0.1s] +✔ | 12 | Multistart method for saem.mmkin models [20.6s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] +✔ | 15 | Plotting [4.7s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [85.7s] +✔ | 1 36 | saemix parent models [30.6s] ──────────────────────────────────────────────────────────────────────────────── 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] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.6s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.9s] +✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 5 | Summary [0.2s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s] -✔ | 9 | Hypothesis tests [8.2s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] +✔ | 5 | Summary +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.9s] +✔ | 9 | Hypothesis tests [3.3s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 280.1 s +Duration: 111.2 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) -- cgit v1.2.1 From a54bd290bc3884d0000c52c1b29bc557825d9eae Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 15 Dec 2022 14:50:28 +0100 Subject: List random effects correlations in output if any Update docs --- log/test.log | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 89265100..dc1b6c74 100644 --- a/log/test.log +++ b/log/test.log @@ -1,11 +1,11 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [1.5s] +✔ | 5 | Analytical solutions for coupled models [1.6s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE ✔ | 12 | Confidence intervals and p-values [0.4s] -✔ | 1 12 | Dimethenamid data from 2018 [12.3s] +✔ | 1 12 | Dimethenamid data from 2018 [12.4s] ──────────────────────────────────────────────────────────────────────────────── 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 @@ -16,23 +16,23 @@ Reason: Fitting this ODE model with saemix takes about 15 minutes on my system ✔ | 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 [18.2s] -✔ | 1 11 | Nonlinear mixed-effects models [5.8s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.1s] +✔ | 1 11 | Nonlinear mixed-effects models [5.9s] ──────────────────────────────────────────────────────────────────────────────── 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 [0.4s] -✔ | 3 | mkinfit features [0.4s] +✔ | 3 | mkinfit features [0.5s] ✔ | 8 | mkinmod model generation and printing ✔ | 3 | Model predictions with mkinpredict [0.1s] -✔ | 12 | Multistart method for saem.mmkin models [20.6s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4s] +✔ | 12 | Multistart method for saem.mmkin models [21.6s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] ✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] -✔ | 15 | Plotting [4.7s] +✔ | 15 | Plotting [4.6s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [30.6s] +✔ | 1 36 | saemix parent models [30.9s] ──────────────────────────────────────────────────────────────────────────────── 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 @@ -47,7 +47,7 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 111.2 s +Duration: 113.6 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 15 minutes on my system (1) -- cgit v1.2.1