ℹ Testing mkin
✔ | F W S  OK | Context
✔ |         5 | AIC calculation
✔ |         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 [1.0s]
✔ |     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 [5.2s]
✔ |         5 | Time step normalisation
✔ |         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 [0.3s]
✔ |         1 | Fitting the logistic model [0.2s]
✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [40.7s]
✖ | 1   1  10 | Nonlinear mixed-effects models [13.2s]
────────────────────────────────────────────────────────────────────────────────
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]
  ""
  "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: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 [0.3s]
✖ | 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
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'): 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 [2.3s]
✔ |         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
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 [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 [3.5s]
✔ |         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 [7.7s]
✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]

══ Results ═════════════════════════════════════════════════════════════════════
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 5 | WARN 0 | SKIP 3 | PASS 265 ]