diff options
| -rw-r--r-- | log/test.log | 32 | ||||
| -rw-r--r-- | log/test_dev.log | 114 | ||||
| -rw-r--r-- | tests/testthat/test_mixed.R | 3 |
3 files changed, 112 insertions, 37 deletions
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 diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R index 8c257738..39a332f5 100644 --- a/tests/testthat/test_mixed.R +++ b/tests/testthat/test_mixed.R @@ -16,7 +16,8 @@ test_that("Print methods work", { expect_known_output(print(sfo_saem_1_reduced, digits = 1), "print_sfo_saem_1_reduced.txt") skip_on_cran() # The following test is platform dependent and fails on - # win-builder with current (18 Nov 2022) R-devel and on the Fedora CRAN check systems + # win-builder with current (18 Nov 2022) R-devel, on the Linux R-devel CRAN check systems + # and also using R-devel locally expect_known_output(print(dfop_saem_1, digits = 1), "print_dfop_saem_1.txt") }) |