Update platform specific tests on desktop

2 files changed, 83 insertions, 34 deletions

diff --git a/log/build.log b/log/build.log
index 717128fd..01173753 100644
--- a/log/build.log
+++ b/log/build.log
@@ -7,4 +7,7 @@
 * checking for empty or unneeded directories
 Removed empty directory ‘mkin/vignettes/web_only’
 * building ‘mkin_1.2.5.tar.gz’
+Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
+  storing paths of more than 100 bytes is not portable:
+  ‘mkin/tests/testthat/_snaps/multistart/mixed-model-fit-for-saem-object-with-mkin-transformations.new.svg’
 
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 ]