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') 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/check.log | 4 ++-- log/test.log | 36 ++++++++++++++++++------------------ 2 files changed, 20 insertions(+), 20 deletions(-) (limited to 'log') diff --git a/log/check.log b/log/check.log index 3fea2ec6..7aa4610c 100644 --- a/log/check.log +++ b/log/check.log @@ -41,7 +41,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [14s/14s] OK +* checking R code for possible problems ... [18s/18s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -57,7 +57,7 @@ Maintainer: ‘Johannes Ranke ’ * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [15s/15s] OK +* checking examples ... [20s/20s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK 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 90354f5cd9e095f9ef98424689a2716770b248d4 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 16 Nov 2022 22:44:34 +0100 Subject: Reduce testing on CRAN servers --- log/build.log | 1 - 1 file changed, 1 deletion(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index c4f9b8a2..a56a64df 100644 --- a/log/build.log +++ b/log/build.log @@ -6,4 +6,3 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘mkin_1.2.0.tar.gz’ - -- cgit v1.2.1 From 9db8338d3a9240ed4685fcdd7aab9692031d5a04 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 05:56:25 +0100 Subject: Improve logLik.mkinfit to attach nobs attribute The lack of that attribute lead to a failure to calculate the BIC in test_AIC.R on R-devel from yesterday. --- log/test_dev.log | 61 +++++++++++++++++++++++++++++--------------------------- 1 file changed, 32 insertions(+), 29 deletions(-) (limited to 'log') diff --git a/log/test_dev.log b/log/test_dev.log index 24905a1a..527d28ed 100644 --- a/log/test_dev.log +++ b/log/test_dev.log @@ -1,54 +1,57 @@ -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 [3.2s] ✔ | 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 [31.3s] ──────────────────────────────────────────────────────────────────────────────── -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] +✔ | 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 [23.5s] +✔ | 1 12 | Nonlinear mixed-effects models [0.3s] ──────────────────────────────────────────────────────────────────────────────── -Skip (test_mixed.R:68:3): saemix results are reproducible for biphasic fits +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] -✔ | 3 | mkinfit features [1.1s] +✔ | 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] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.7s] -✔ | 16 | Plotting [1.4s] +✔ | 9 | Multistart method for saem.mmkin models [35.2s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s] +✔ | 16 | Plotting [10.0s] ✔ | 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 [63.3s] +──────────────────────────────────────────────────────────────────────────────── +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 [1.3s] +✔ | 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) [2.1s] +✔ | 9 | Hypothesis tests [7.5s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 315.9 s +Duration: 204.4 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 0 | WARN 0 | SKIP 3 | PASS 269 ] -- 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/build.log | 1 + log/test.log | 38 +++++++++++++++++++------------------- 2 files changed, 20 insertions(+), 19 deletions(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index a56a64df..c4f9b8a2 100644 --- a/log/build.log +++ b/log/build.log @@ -6,3 +6,4 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘mkin_1.2.0.tar.gz’ + 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/build.log | 2 +- log/test.log | 20 ++++++++++---------- 2 files changed, 11 insertions(+), 11 deletions(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index c4f9b8a2..6be01938 100644 --- a/log/build.log +++ b/log/build.log @@ -5,5 +5,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.2.0.tar.gz’ +* building ‘mkin_1.2.1.tar.gz’ 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/check.log | 4 ++-- log/test.log | 28 ++++++++++++++-------------- 2 files changed, 16 insertions(+), 16 deletions(-) (limited to 'log') diff --git a/log/check.log b/log/check.log index 7aa4610c..31fc31eb 100644 --- a/log/check.log +++ b/log/check.log @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.0’ +* this is package ‘mkin’ version ‘1.2.1’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ @@ -41,7 +41,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [18s/18s] OK +* checking R code for possible problems ... [17s/17s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK 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') 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') 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 ++++++++-------- log/test_dev.log | 114 +++++++++++++++++++++++++++++++++++++++++++++---------- 2 files changed, 110 insertions(+), 36 deletions(-) (limited to '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) diff --git a/log/test_dev.log b/log/test_dev.log index 527d28ed..1612e32d 100644 --- a/log/test_dev.log +++ b/log/test_dev.log @@ -1,57 +1,131 @@ 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 [31.3s] +✔ | 12 | Confidence intervals and p-values [1.1s] +✔ | 1 12 | Dimethenamid data from 2018 [33.8s] ──────────────────────────────────────────────────────────────────────────────── 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 [5.2s] +✔ | 14 | Error model fitting [5.7s] ✔ | 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 [23.5s] -✔ | 1 12 | Nonlinear mixed-effects models [0.3s] +✖ | 1 9 | Batch fitting and diagnosing hierarchical kinetic models [25.5s] ──────────────────────────────────────────────────────────────────────────────── -Skip ('test_mixed.R:74'): saemix results are reproducible for biphasic fits +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 +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: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 [0.5s] -✔ | 3 | mkinfit features [0.7s] +✔ | 3 | mkinfit features [0.8s] ✔ | 8 | mkinmod model generation and printing [0.2s] ✔ | 3 | Model predictions with mkinpredict [0.3s] -✔ | 9 | Multistart method for saem.mmkin models [35.2s] +✖ | 4 8 | Multistart method for saem.mmkin models [53.5s] +──────────────────────────────────────────────────────────────────────────────── +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: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 +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 [2.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [8.3s] -✔ | 16 | Plotting [10.0s] +✔ | 9 | Nonlinear mixed-effects models with nlme [9.2s] +✖ | 1 14 | Plotting [10.5s] +──────────────────────────────────────────────────────────────────────────────── +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 -✔ | 1 36 | saemix parent models [63.3s] +✔ | 1 36 | saemix parent models [74.3s] ──────────────────────────────────────────────────────────────────────────────── 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 [1.3s] +✔ | 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] +✔ | 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) [2.1s] -✔ | 9 | Hypothesis tests [7.5s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s] +✔ | 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] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 204.4 s +Duration: 256.2 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) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 3 | PASS 269 ] +[ FAIL 7 | WARN 0 | SKIP 3 | PASS 263 ] +Error while shutting down parallel: unable to terminate some child processes -- 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/build.log | 2 +- log/test.log | 34 +++++++++++++++++----------------- 2 files changed, 18 insertions(+), 18 deletions(-) (limited to 'log') diff --git a/log/build.log b/log/build.log index 6be01938..dbe0cd5b 100644 --- a/log/build.log +++ b/log/build.log @@ -5,5 +5,5 @@ * creating vignettes ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories -* building ‘mkin_1.2.1.tar.gz’ +* building ‘mkin_1.2.2.tar.gz’ 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/check.log | 8 ++++---- log/test.log | 48 ++++++++++++++++++++++++------------------------ 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'log') diff --git a/log/check.log b/log/check.log index 31fc31eb..42365918 100644 --- a/log/check.log +++ b/log/check.log @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘1.2.1’ +* this is package ‘mkin’ version ‘1.2.2’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ @@ -18,7 +18,7 @@ Maintainer: ‘Johannes Ranke ’ * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK -* checking whether package ‘mkin’ can be installed ... OK +* checking whether package ‘mkin’ can be installed ... [11s/11s] OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -41,7 +41,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [17s/17s] OK +* checking R code for possible problems ... [19s/19s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -57,7 +57,7 @@ Maintainer: ‘Johannes Ranke ’ * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [20s/20s] OK +* checking examples ... [24s/24s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK 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') 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 63d29da946192b3191540d549836167334e38ced Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 2 Dec 2022 13:56:01 +0100 Subject: Update test log with current R-devel One printout and four plots are different using current R-devel. These are currently skipped on CRAN. These test were run with the development version of saemix (my branch installable_dev_version). If saemix from CRAN is used, there are some more differences due to different error model parameters --- log/test_dev.log | 65 ++++++++++++++++++++------------------------------------ 1 file changed, 23 insertions(+), 42 deletions(-) (limited to 'log') 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 ] -- 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') 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') 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') 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') 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 From 886c9ef013124aa954d960c655b349b5340ff154 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 19 Dec 2022 12:31:56 +0100 Subject: Rename template folder, create format Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of. --- log/check.log | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) (limited to 'log') diff --git a/log/check.log b/log/check.log index 42365918..aec61e33 100644 --- a/log/check.log +++ b/log/check.log @@ -1,5 +1,5 @@ * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ -* using R version 4.2.2 (2022-10-31) +* using R version 4.2.2 Patched (2022-11-10 r83330) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ @@ -18,7 +18,7 @@ Maintainer: ‘Johannes Ranke ’ * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK -* checking whether package ‘mkin’ can be installed ... [11s/11s] OK +* checking whether package ‘mkin’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for future file timestamps ... OK @@ -41,7 +41,14 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... [19s/19s] OK +* checking R code for possible problems ... NOTE +parplot.multistart.saem.mmkin: no visible global function definition + for ‘quantile’ +Undefined global functions or variables: + quantile +Consider adding + importFrom("stats", "quantile") +to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -57,7 +64,7 @@ Maintainer: ‘Johannes Ranke ’ * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [24s/24s] OK +* checking examples ... [11s/11s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -69,5 +76,9 @@ Maintainer: ‘Johannes Ranke ’ * checking for detritus in the temp directory ... OK * DONE -Status: OK +Status: 1 NOTE +See + ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ +for details. + -- cgit v1.2.1 From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Jan 2023 06:22:04 +0100 Subject: Prebuilt PDF vignettes, summary_listing --- log/check.log | 34 ++++++++++++++++++++++------------ 1 file changed, 22 insertions(+), 12 deletions(-) (limited to 'log') diff --git a/log/check.log b/log/check.log index aec61e33..a81475d9 100644 --- a/log/check.log +++ b/log/check.log @@ -7,11 +7,28 @@ * checking extension type ... Package * this is package ‘mkin’ version ‘1.2.2’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers +* checking CRAN incoming feasibility ... NOTE Maintainer: ‘Johannes Ranke ’ + +Size of tarball: 6636884 bytes * checking package namespace information ... OK * checking package dependencies ... OK -* checking if this is a source package ... OK +* checking if this is a source package ... NOTE +Found the following apparent object files/libraries: + vignettes/2022_wp_1/cyan_dlls/dfop_path_1.so + vignettes/2022_wp_1/cyan_dlls/dfop_path_2.so + vignettes/2022_wp_1/cyan_dlls/fomc_path_1.so + vignettes/2022_wp_1/cyan_dlls/fomc_path_2.so + vignettes/2022_wp_1/cyan_dlls/hs_path_1.so + vignettes/2022_wp_1/cyan_dlls/sfo_path_1.so + vignettes/2022_wp_1/cyan_dlls/sforb_path_1.so + vignettes/2022_wp_1/cyan_dlls/sforb_path_2.so + vignettes/2022_wp_1/dmta_dlls/m_dfop_path.so + vignettes/2022_wp_1/dmta_dlls/m_fomc_path.so + vignettes/2022_wp_1/dmta_dlls/m_hs_path.so + vignettes/2022_wp_1/dmta_dlls/m_sfo_path.so + vignettes/2022_wp_1/dmta_dlls/m_sforb_path.so +Object files/libraries should not be included in a source package. * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK @@ -41,14 +58,7 @@ Maintainer: ‘Johannes Ranke ’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK -* checking R code for possible problems ... NOTE -parplot.multistart.saem.mmkin: no visible global function definition - for ‘quantile’ -Undefined global functions or variables: - quantile -Consider adding - importFrom("stats", "quantile") -to your NAMESPACE file. +* checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK @@ -64,7 +74,7 @@ to your NAMESPACE file. * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... [11s/11s] OK +* checking examples ... [10s/10s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -76,7 +86,7 @@ to your NAMESPACE file. * checking for detritus in the temp directory ... OK * DONE -Status: 1 NOTE +Status: 2 NOTEs See ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ for details. -- cgit v1.2.1