From 9901675e499226eec6304113eb5ffa3b900942c2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 09:03:53 +0200 Subject: Update platform specific tests on desktop --- log/test.log | 114 +++++++++++++++++++++++++++++++++++++++++------------------ 1 file changed, 80 insertions(+), 34 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index c872cb1d..72234347 100644 --- a/log/test.log +++ b/log/test.log @@ -1,50 +1,96 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.1s] +✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [5.3s] -✔ | 12 | Confidence intervals and p-values -✔ | 1 12 | Dimethenamid data from 2018 [31.5s] -✔ | 14 | Error model fitting [5.6s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] +✔ | 12 | Confidence intervals and p-values [0.4s] +✔ | 1 12 | Dimethenamid data from 2018 [12.9s] +──────────────────────────────────────────────────────────────────────────────── +Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data +Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system +──────────────────────────────────────────────────────────────────────────────── +✔ | 14 | Error model fitting [2.3s] ✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) -✔ | 4 | Test fitting the decline of metabolites from their maximum -✔ | 1 | Fitting the logistic model -✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [43.1s] -✔ | 2 16 | Nonlinear mixed-effects models [441.3s] +✔ | 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 [19.0s] +✔ | 2 16 | Nonlinear mixed-effects models [148.3s] +──────────────────────────────────────────────────────────────────────────────── +Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits +Reason: Fitting with saemix takes around 10 minutes when using deSolve + +Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work +Reason: This is seldom used, so save some time +──────────────────────────────────────────────────────────────────────────────── ✔ | 3 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls -✔ | 3 | mkinfit features +✔ | 10 | Special cases of mkinfit calls [0.3s] +✔ | 3 | mkinfit features [0.5s] ✔ | 8 | mkinmod model generation and printing -✔ | 3 | Model predictions with mkinpredict -✔ | 12 | Multistart method for saem.mmkin models [71.6s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.7s] -✔ | 9 | Nonlinear mixed-effects models with nlme [10.1s] -✔ | 15 | Plotting [12.1s] +✔ | 3 | Model predictions with mkinpredict [0.1s] +✖ | 3 9 | Multistart method for saem.mmkin models [22.9s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_multistart.R:44:3'): 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:55:3'): 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:56:3'): 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 [1.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] +✖ | 1 14 | Plotting [4.6s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_plot.R:55:3'): 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 [81.8s] -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] +✔ | 1 36 | saemix parent models [31.2s] +──────────────────────────────────────────────────────────────────────────────── +Skip ('test_saemix_parent.R:143:3'): 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 [0.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [3.8s] +✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s] -✔ | 9 | Hypothesis tests [7.3s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.5s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 9 | Hypothesis tests [2.9s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 731.0 s +Duration: 260.5 s -── Skipped tests (4) ─────────────────────────────────────────────────────────── -• Fitting this ODE model with saemix takes about 15 minutes on my system (1): - 'test_dmta.R:88:3' -• Fitting with saemix takes around 10 minutes when using deSolve (1): - 'test_mixed.R:80:3' -• This is seldom used, so save some time (1): 'test_mixed.R:133:3' -• This still takes almost 2.5 minutes although we do not solve ODEs (1): - 'test_saemix_parent.R:143:3' +── Skipped tests ────────────────────────────────────────────────────────────── +• Fitting this ODE model with saemix takes about 5 minutes on my new system (1) +• Fitting with saemix takes around 10 minutes when using deSolve (1) +• This is seldom used, so save some time (1) +• This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ] +[ FAIL 4 | WARN 0 | SKIP 4 | PASS 277 ] -- cgit v1.2.1 From 49f7538f342e504d3f62faa40ca0b819ed642335 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 09:12:24 +0200 Subject: Update test log with libopenblas0-pthread --- log/test.log | 64 ++++++++++++++---------------------------------------------- 1 file changed, 15 insertions(+), 49 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index 72234347..b36c62cd 100644 --- a/log/test.log +++ b/log/test.log @@ -1,12 +1,12 @@ 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 -✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] ✔ | 12 | Confidence intervals and p-values [0.4s] -✔ | 1 12 | Dimethenamid data from 2018 [12.9s] +✔ | 1 12 | Dimethenamid data from 2018 [12.8s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system @@ -17,8 +17,8 @@ Reason: Fitting this ODE model with saemix takes about 5 minutes on my new syste ✔ | 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 [19.0s] -✔ | 2 16 | Nonlinear mixed-effects models [148.3s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.5s] +✔ | 2 16 | Nonlinear mixed-effects models [148.1s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_mixed.R:80:3'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -29,55 +29,21 @@ Reason: This is seldom used, so save some time ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls [0.3s] ✔ | 3 | mkinfit features [0.5s] -✔ | 8 | mkinmod model generation and printing -✔ | 3 | Model predictions with mkinpredict [0.1s] -✖ | 3 9 | Multistart method for saem.mmkin models [22.9s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_multistart.R:44:3'): 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:55:3'): 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:56:3'): 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 [1.5s] -✔ | 9 | Nonlinear mixed-effects models with nlme [3.7s] -✖ | 1 14 | Plotting [4.6s] -──────────────────────────────────────────────────────────────────────────────── -Failure ('test_plot.R:55:3'): 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(...) -──────────────────────────────────────────────────────────────────────────────── +✔ | 8 | mkinmod model generation and printing [0.1s] +✔ | 3 | Model predictions with mkinpredict [0.2s] +✔ | 12 | Multistart method for saem.mmkin models [28.4s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.6s] +✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] +✔ | 15 | Plotting [4.6s] ✔ | 4 | Residuals extracted from mkinfit models -✔ | 1 36 | saemix parent models [31.2s] +✔ | 1 36 | saemix parent models [31.0s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143:3'): 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 [0.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.7s] +✔ | 10 | Fitting the SFORB model [1.8s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] @@ -85,7 +51,7 @@ 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: 260.5 s +Duration: 266.7 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system (1) @@ -93,4 +59,4 @@ Duration: 260.5 s • This is seldom used, so save some time (1) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 4 | WARN 0 | SKIP 4 | PASS 277 ] +[ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ] -- cgit v1.2.1 From bbed90f6a4010ac0b911ec13c04ae06eebc74bb5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Aug 2023 09:23:27 +0200 Subject: Update tests without any openblas variant This even a bit faster. --- log/test.log | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++---------- 1 file changed, 69 insertions(+), 14 deletions(-) (limited to 'log/test.log') diff --git a/log/test.log b/log/test.log index b36c62cd..6d5bc470 100644 --- a/log/test.log +++ b/log/test.log @@ -1,25 +1,46 @@ ℹ Testing mkin ✔ | F W S OK | Context ✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [1.6s] +✔ | 5 | Analytical solutions for coupled models [1.5s] ✔ | 5 | Calculation of Akaike weights ✔ | 3 | Export dataset for reading into CAKE -✔ | 6 | Use of precompiled symbols in mkinpredict [3.3s] +✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s] ✔ | 12 | Confidence intervals and p-values [0.4s] -✔ | 1 12 | Dimethenamid data from 2018 [12.8s] +✔ | 1 12 | Dimethenamid data from 2018 [13.2s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_dmta.R:88:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data Reason: Fitting this ODE model with saemix takes about 5 minutes on my new system ──────────────────────────────────────────────────────────────────────────────── -✔ | 14 | Error model fitting [2.3s] +✔ | 14 | Error model fitting [2.5s] ✔ | 5 | Time step normalisation ✔ | 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 [19.5s] -✔ | 2 16 | Nonlinear mixed-effects models [148.1s] +✔ | 10 | Batch fitting and diagnosing hierarchical kinetic models [19.0s] +✖ | 1 2 15 | Nonlinear mixed-effects models [149.2s] ──────────────────────────────────────────────────────────────────────────────── +Failure ('test_mixed.R:21:3'): 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:80:3'): saemix results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve @@ -29,21 +50,55 @@ Reason: This is seldom used, so save some time ✔ | 3 | Test dataset classes mkinds and mkindsg ✔ | 10 | Special cases of mkinfit calls [0.3s] ✔ | 3 | mkinfit features [0.5s] -✔ | 8 | mkinmod model generation and printing [0.1s] -✔ | 3 | Model predictions with mkinpredict [0.2s] -✔ | 12 | Multistart method for saem.mmkin models [28.4s] +✔ | 8 | mkinmod model generation and printing +✔ | 3 | Model predictions with mkinpredict [0.1s] +✖ | 3 9 | Multistart method for saem.mmkin models [23.2s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_multistart.R:44:3'): 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:55:3'): 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:56:3'): 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 [1.6s] ✔ | 9 | Nonlinear mixed-effects models with nlme [3.8s] -✔ | 15 | Plotting [4.6s] +✖ | 1 14 | Plotting [4.7s] +──────────────────────────────────────────────────────────────────────────────── +Failure ('test_plot.R:55:3'): 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 [31.0s] +✔ | 1 36 | saemix parent models [31.4s] ──────────────────────────────────────────────────────────────────────────────── Skip ('test_saemix_parent.R:143:3'): 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 [0.5s] ✔ | 11 | Processing of residue series -✔ | 10 | Fitting the SFORB model [1.8s] +✔ | 10 | Fitting the SFORB model [1.7s] ✔ | 1 | Summaries of old mkinfit objects ✔ | 5 | Summary ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s] @@ -51,7 +106,7 @@ 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: 266.7 s +Duration: 262.6 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting this ODE model with saemix takes about 5 minutes on my new system (1) @@ -59,4 +114,4 @@ Duration: 266.7 s • This is seldom used, so save some time (1) • This still takes almost 2.5 minutes although we do not solve ODEs (1) -[ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ] +[ FAIL 5 | WARN 0 | SKIP 4 | PASS 276 ] -- cgit v1.2.1