aboutsummaryrefslogtreecommitdiff
path: root/log
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2023-08-17 09:23:27 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-08-17 09:23:27 +0200
commitbbed90f6a4010ac0b911ec13c04ae06eebc74bb5 (patch)
tree83f6d3434d1e39eaccb21a346da0e35f217de248 /log
parent49f7538f342e504d3f62faa40ca0b819ed642335 (diff)
Update tests without any openblas variant
This even a bit faster.
Diffstat (limited to 'log')
-rw-r--r--log/build.log3
-rw-r--r--log/test.log83
2 files changed, 69 insertions, 17 deletions
diff --git a/log/build.log b/log/build.log
index 01173753..717128fd 100644
--- a/log/build.log
+++ b/log/build.log
@@ -7,7 +7,4 @@
* 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 b36c62cd..6d5bc470 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,25 +1,46 @@
ℹ Testing mkin
✔ | F W S OK | Context
✔ | 5 | AIC calculation
-✔ | 5 | Analytical solutions for coupled models [1.6s]
+✔ | 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 [3.3s]
+✔ | 6 | Use of precompiled symbols in mkinpredict [3.1s]
✔ | 12 | Confidence intervals and p-values [0.4s]
-✔ | 1 12 | Dimethenamid data from 2018 [12.8s]
+✔ | 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 [2.3s]
+✔ | 14 | Error model fitting [2.5s]
✔ | 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 [19.5s]
-✔ | 2 16 | Nonlinear mixed-effects models [148.1s]
+✔ | 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
@@ -29,21 +50,55 @@ Reason: This is seldom used, so save some time
✔ | 3 | Test dataset classes mkinds and mkindsg
✔ | 10 | Special cases of mkinfit calls [0.3s]
✔ | 3 | mkinfit features [0.5s]
-✔ | 8 | mkinmod model generation and printing [0.1s]
-✔ | 3 | Model predictions with mkinpredict [0.2s]
-✔ | 12 | Multistart method for saem.mmkin models [28.4s]
+✔ | 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]
-✔ | 15 | Plotting [4.6s]
+✖ | 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(...)
+────────────────────────────────────────────────────────────────────────────────
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 1 36 | saemix parent models [31.0s]
+✔ | 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]
✔ | 11 | Processing of residue series
-✔ | 10 | Fitting the SFORB model [1.8s]
+✔ | 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) [0.8s]
@@ -51,7 +106,7 @@ Reason: This still takes almost 2.5 minutes although we do not solve ODEs
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 266.7 s
+Duration: 262.6 s
── Skipped tests ──────────────────────────────────────────────────────────────
• Fitting this ODE model with saemix takes about 5 minutes on my new system (1)
@@ -59,4 +114,4 @@ Duration: 266.7 s
• 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 5 | WARN 0 | SKIP 4 | PASS 276 ]

Contact - Imprint