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authorJohannes Ranke <jranke@uni-bremen.de>2023-08-29 14:28:18 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-08-29 14:29:13 +0200
commita47f458cf4b2433cdc9a75f62cb1d9fb2287d083 (patch)
treeabe0e1230b7e6e57de78797abecf69a7eee359ab /log
parentebfb381f37df391d7f641ff2ceffb6698e3ea860 (diff)
Run tests on slimbook: 573.5 sHEADdev
Compared with 262.6 s on my main desktop
Diffstat (limited to 'log')
-rw-r--r--log/test.log139
1 files changed, 36 insertions, 103 deletions
diff --git a/log/test.log b/log/test.log
index 6d5bc470..461e6868 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,117 +1,50 @@
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 [2.4s]
✔ | 5 | Calculation of Akaike weights
✔ | 3 | Export dataset for reading into CAKE
-✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s]
-✔ | 12 | Confidence intervals and p-values [0.4s]
-✔ | 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 [2.5s]
+✔ | 6 | Use of precompiled symbols in mkinpredict [5.7s]
+✔ | 12 | Confidence intervals and p-values
+✔ | 1 12 | Dimethenamid data from 2018 [25.0s]
+✔ | 14 | Error model fitting [5.3s]
✔ | 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 [19.0s]
-✖ | 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
-
-Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work
-Reason: This is seldom used, so save some time
-────────────────────────────────────────────────────────────────────────────────
+✔ | 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 [39.8s]
+✔ | 2 16 | Nonlinear mixed-effects models [351.2s]
✔ | 3 | Test dataset classes mkinds and mkindsg
-✔ | 10 | Special cases of mkinfit calls [0.3s]
-✔ | 3 | mkinfit features [0.5s]
+✔ | 10 | Special cases of mkinfit calls
+✔ | 3 | mkinfit features
✔ | 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]
-✖ | 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(...)
-────────────────────────────────────────────────────────────────────────────────
+✔ | 3 | Model predictions with mkinpredict
+✔ | 12 | Multistart method for saem.mmkin models [52.7s]
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [2.1s]
+✔ | 9 | Nonlinear mixed-effects models with nlme [7.7s]
+✔ | 15 | Plotting [8.2s]
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 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]
+✔ | 1 36 | saemix parent models [56.3s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [1.7s]
+✔ | 10 | Fitting the SFORB model [2.6s]
✔ | 1 | Summaries of old mkinfit objects
✔ | 5 | Summary
-✔ | 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]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.4s]
+✔ | 9 | Hypothesis tests [6.1s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [1.4s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 262.6 s
-
-── 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 5 | WARN 0 | SKIP 4 | PASS 276 ]
+Duration: 573.5 s
+
+── Skipped tests (4) ───────────────────────────────────────────────────────────
+• Fitting this ODE model with saemix takes about 5 minutes on my new 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'
+
+[ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ]

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