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-rw-r--r--test.log39
1 files changed, 22 insertions, 17 deletions
diff --git a/test.log b/test.log
index 79813341..58c819f4 100644
--- a/test.log
+++ b/test.log
@@ -2,40 +2,45 @@ Loading mkin
Testing mkin
✔ | OK F W S | Context
⠏ | 0 | Export dataset for reading into CAKE ⠋ | 1 | Export dataset for reading into CAKE ✔ | 1 | Export dataset for reading into CAKE
- ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ✔ | 2 | Calculation of FOCUS chi2 error levels [2.4 s]
- ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [8.0 s]
- ⠏ | 0 | Test fitting the decline of metabolites from their maximum ⠋ | 1 | Test fitting the decline of metabolites from their maximum ⠙ | 2 | Test fitting the decline of metabolites from their maximum ⠹ | 3 | Test fitting the decline of metabolites from their maximum ✔ | 3 | Test fitting the decline of metabolites from their maximum [0.6 s]
- ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting ⠹ | 2 1 | Iteratively reweighted least squares (IRLS) fitting ✔ | 2 1 | Iteratively reweighted least squares (IRLS) fitting [16.0 s]
+ ⠏ | 0 | Error model fitting ⠋ | 1 | Error model fitting ⠙ | 2 | Error model fitting ⠹ | 3 | Error model fitting ⠸ | 4 | Error model fitting ⠼ | 5 | Error model fitting ⠴ | 6 | Error model fitting ⠦ | 7 | Error model fitting ⠧ | 8 | Error model fitting ⠇ | 9 | Error model fitting ⠏ | 9 1 | Error model fitting ⠋ | 10 1 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 | Error model fitting ⠙ | 10 2 ⠙ | 10 | Error model fitting2 | Error model fitting ⠙ | 11 1 | Error model fitting ⠹ | 12 1 | Error model fitting ✔ | 12 1 | Error model fitting [163.7 s]
────────────────────────────────────────────────────────────────────────────────
-test_irls.R:48: skip: Reweighting method 'tc' works
-Too much trouble with datasets that are randomly generated
+test_error_models.R:148: warning: Reweighting method 'tc' produces reasonable variance estimates
+Observations with value of zero were removed from the data
────────────────────────────────────────────────────────────────────────────────
- ⠏ | 0 | Fitting the logistic model ⠋ | 1 | Fitting the logistic model ⠙ | 1 1 | Fitting the logistic model ✔ | 1 1 | Fitting the logistic model [0.5 s]
+ ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ⠹ | 3 | Calculation of FOCUS chi2 error levels ✔ | 3 | Calculation of FOCUS chi2 error levels [2.4 s]
+ ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 13 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 13 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [8.3 s]
+────────────────────────────────────────────────────────────────────────────────
+test_FOCUS_D_UBA_expertise.R:89: skip: The t-value for fits using internal transformations corresponds with results from FME, synthetic data
+Hessian matrices and df calculations differ from those in FME
+────────────────────────────────────────────────────────────────────────────────
+ ⠏ | 0 | Test fitting the decline of metabolites from their maximum ⠋ | 1 | Test fitting the decline of metabolites from their maximum ⠙ | 2 | Test fitting the decline of metabolites from their maximum ⠹ | 3 | Test fitting the decline of metabolites from their maximum ⠸ | 4 | Test fitting the decline of metabolites from their maximum ⠼ | 5 | Test fitting the decline of metabolites from their maximum ⠴ | 6 | Test fitting the decline of metabolites from their maximum ✔ | 6 | Test fitting the decline of metabolites from their maximum [0.9 s]
+ ⠏ | 0 | Fitting the logistic model ⠋ | 1 | Fitting the logistic model ⠙ | 1 1 | Fitting the logistic model ✔ | 1 1 | Fitting the logistic model [0.9 s]
────────────────────────────────────────────────────────────────────────────────
test_logistic.R:41: skip: The logistic fit can be done via differential equation
Skip slow fit of logistic model using deSolve without compilation
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | Test dataset class mkinds used in gmkin ⠋ | 1 | Test dataset class mkinds used in gmkin ✔ | 1 | Test dataset class mkinds used in gmkin
- ⠏ | 0 | Special cases of mkinfit calls ⠋ | 1 | Special cases of mkinfit calls ⠙ | 2 | Special cases of mkinfit calls ⠹ | 3 | Special cases of mkinfit calls ⠸ | 4 | Special cases of mkinfit calls ⠼ | 5 | Special cases of mkinfit calls ⠴ | 6 | Special cases of mkinfit calls ⠦ | 7 | Special cases of mkinfit calls ⠧ | 8 | Special cases of mkinfit calls ⠇ | 9 | Special cases of mkinfit calls ⠏ | 10 | Special cases of mkinfit calls ⠋ | 11 | Special cases of mkinfit calls ⠙ | 12 | Special cases of mkinfit calls ⠹ | 12 1 | Special cases of mkinfit calls ⠸ | 13 1 | Special cases of mkinfit calls ⠼ | 14 1 | Special cases of mkinfit calls ⠴ | 15 1 | Special cases of mkinfit calls ⠦ | 16 1 | Special cases of mkinfit calls ✔ | 16 1 | Special cases of mkinfit calls [2.9 s]
+ ⠏ | 0 | Special cases of mkinfit calls ⠋ | 1 | Special cases of mkinfit calls ⠙ | 2 | Special cases of mkinfit calls ⠹ | 3 | Special cases of mkinfit calls ⠸ | 4 | Special cases of mkinfit calls ⠼ | 5 | Special cases of mkinfit calls ⠴ | 6 | Special cases of mkinfit calls ⠦ | 7 | Special cases of mkinfit calls ⠧ | 8 | Special cases of mkinfit calls ⠇ | 8 1 | Special cases of mkinfit calls ⠏ | 9 1 | Special cases of mkinfit calls ⠋ | 10 1 | Special cases of mkinfit calls ⠙ | 11 1 | Special cases of mkinfit calls ⠹ | 12 1 | Special cases of mkinfit calls ✔ | 12 1 | Special cases of mkinfit calls [3.2 s]
────────────────────────────────────────────────────────────────────────────────
-test_mkinfit_errors.R:67: skip: mkinfit warns if the user chooses the SANN method
-The SANN algorithm takes very long with the default maximum number of iterations of 10000
+test_mkinfit_errors.R:59: warning: mkinfit stops early when a low maximum number of iterations is specified
+Optimisation did not converge:
+iteration limit reached without convergence (10)
────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | mkinmod model generation and printing ⠋ | 1 | mkinmod model generation and printing ⠙ | 2 | mkinmod model generation and printing ⠹ | 3 | mkinmod model generation and printing ⠸ | 4 | mkinmod model generation and printing ⠼ | 5 | mkinmod model generation and printing ⠴ | 6 | mkinmod model generation and printing ⠦ | 7 | mkinmod model generation and printing ⠧ | 8 | mkinmod model generation and printing ⠇ | 9 | mkinmod model generation and printing ✔ | 9 | mkinmod model generation and printing [0.2 s]
⠏ | 0 | Model predictions with mkinpredict ⠋ | 1 | Model predictions with mkinpredict ⠙ | 2 | Model predictions with mkinpredict ⠹ | 3 | Model predictions with mkinpredict ✔ | 3 | Model predictions with mkinpredict [0.3 s]
- ⠏ | 0 | Evaluations according to 2015 NAFTA guidance ⠋ | 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 2 | Evaluations according to 2015 NAFTA guidance ⠹ | 3 | Evaluations according to 2015 NAFTA guidance ⠸ | 4 | Evaluations according to 2015 NAFTA guidance ⠼ | 5 | Evaluations according to 2015 NAFTA guidance ⠴ | 6 | Evaluations according to 2015 NAFTA guidance ⠦ | 7 | Evaluations according to 2015 NAFTA guidance ⠧ | 8 | Evaluations according to 2015 NAFTA guidance ⠇ | 9 | Evaluations according to 2015 NAFTA guidance ⠏ | 10 | Evaluations according to 2015 NAFTA guidance ⠋ | 11 | Evaluations according to 2015 NAFTA guidance ⠙ | 12 | Evaluations according to 2015 NAFTA guidance ⠹ | 13 | Evaluations according to 2015 NAFTA guidance ⠸ | 14 | Evaluations according to 2015 NAFTA guidance ⠼ | 15 | Evaluations according to 2015 NAFTA guidance ⠴ | 16 | Evaluations according to 2015 NAFTA guidance ⠦ | 17 | Evaluations according to 2015 NAFTA guidance ✔ | 17 | Evaluations according to 2015 NAFTA guidance [2.2 s]
- ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [23.8 s]
+ ⠏ | 0 | Evaluations according to 2015 NAFTA guidance ⠋ | 1 | Evaluations according to 2015 NAFTA guidance ⠙ | 2 | Evaluations according to 2015 NAFTA guidance ⠹ | 3 | Evaluations according to 2015 NAFTA guidance ⠸ | 4 | Evaluations according to 2015 NAFTA guidance ⠼ | 5 | Evaluations according to 2015 NAFTA guidance ⠴ | 6 | Evaluations according to 2015 NAFTA guidance ⠦ | 7 | Evaluations according to 2015 NAFTA guidance ⠧ | 8 | Evaluations according to 2015 NAFTA guidance ⠇ | 9 | Evaluations according to 2015 NAFTA guidance ⠏ | 10 | Evaluations according to 2015 NAFTA guidance ⠋ | 11 | Evaluations according to 2015 NAFTA guidance ⠙ | 12 | Evaluations according to 2015 NAFTA guidance ⠹ | 13 | Evaluations according to 2015 NAFTA guidance ⠸ | 14 | Evaluations according to 2015 NAFTA guidance ⠼ | 15 | Evaluations according to 2015 NAFTA guidance ⠴ | 16 | Evaluations according to 2015 NAFTA guidance ✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s]
+ ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [58.6 s]
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs) ⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs) ⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs) ⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs) ⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [3.7 s]
⠏ | 0 | Summary ⠋ | 1 | Summary ✔ | 1 | Summary
⠏ | 0 | Plotting ⠋ | 1 | Plotting ⠙ | 2 | Plotting ⠹ | 3 | Plotting ⠸ | 4 | Plotting ✔ | 4 | Plotting [0.3 s]
⠏ | 0 | AIC calculation ⠋ | 1 | AIC calculation ⠙ | 2 | AIC calculation ✔ | 2 | AIC calculation
- ⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.9 s]
+ ⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.6 s]
⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.4 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 75.3 s
+Duration: 265.8 s
-OK: 106
+OK: 115
Failed: 0
-Warnings: 0
-Skipped: 3
+Warnings: 2
+Skipped: 2

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