Update tests on 5950x

Update platform dependent test plots

2 files changed, 37 insertions, 44 deletions

diff --git a/log/check.log b/log/check.log
index f7a0d87e..9f05935f 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,5 +1,5 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.2.2 (2022-10-31)
+* using R version 4.2.3 (2023-03-15)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
@@ -10,9 +10,7 @@
 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking package namespace information ... OK
-* checking package dependencies ...Warning: unable to access index for repository https://cran.rstudio.com/src/contrib:
-  cannot open URL 'https://cran.rstudio.com/src/contrib/PACKAGES'
- OK
+* checking package dependencies ... OK
 * checking if this is a source package ... OK
 * checking if there is a namespace ... OK
 * checking for executable files ... OK
@@ -23,8 +21,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking whether package ‘mkin’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
-* checking for future file timestamps ... NOTE
-unable to verify current time
+* checking for future file timestamps ... OK
 * checking ‘build’ directory ... OK
 * checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
@@ -44,7 +41,7 @@ unable to verify current time
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [14s/14s] OK
+* checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -61,21 +58,17 @@ unable to verify current time
 * checking sizes of PDF files under ‘inst/doc’ ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... [18s/18s] OK
+* checking examples ... [11s/11s] OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in ‘inst/doc’ ... OK
-* checking re-building of vignette outputs ... [11s/11s] OK
+* checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
-* skipping checking HTML version of manual: no command ‘tidy’ found
+* checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 1 NOTE
-See
-  ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
-for details.
-
+Status: OK
 
diff --git a/log/test.log b/log/test.log
index d3939c0f..de28f836 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,53 +1,53 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [2.8s]
+✔ |         5 | Analytical solutions for coupled models [1.6s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
-✔ |        12 | Confidence intervals and p-values [0.9s]
-✔ |     1  12 | Dimethenamid data from 2018 [30.7s]
+✔ |        12 | Confidence intervals and p-values [0.4s]
+✔ |     1  12 | Dimethenamid data from 2018 [12.0s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_dmta.R:99:3'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+Skip ('test_dmta.R:99'): 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 [6.9s]
+✔ |        14 | Error model fitting [2.3s]
 ✔ |         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) [0.7s]
-✔ |         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 [42.7s]
-✔ |     1  11 | Nonlinear mixed-effects models [13.3s]
+✔ |         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]
+✔ |     1  11 | Nonlinear mixed-effects models [5.9s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_mixed.R:78:3'): saemix results are reproducible for biphasic fits
+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 [0.6s]
-✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |        12 | Multistart method for saem.mmkin models [73.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.0s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [1107.1s]
-✔ |        15 | Plotting [13.3s]
+✔ |        10 | Special cases of mkinfit calls [0.5s]
+✔ |         3 | mkinfit features [0.5s]
+✔ |         8 | mkinmod model generation and printing
+✔ |         3 | Model predictions with mkinpredict [0.1s]
+✔ |        12 | Multistart method for saem.mmkin models [21.7s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [3.7s]
+✔ |        15 | Plotting [4.9s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [74.8s]
+✔ |     1  36 | saemix parent models [32.6s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_saemix_parent.R:143:3'): We can also use mkin solution methods for saem
+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]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [0.5s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [3.3s]
+✔ |        10 | Fitting the SFORB model [1.7s]
 ✔ |         1 | Summaries of old mkinfit objects
-✔ |         5 | Summary [0.1s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.8s]
-✔ |         9 | Hypothesis tests [6.1s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [1.8s]
+✔ |         5 | Summary
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [0.8s]
+✔ |         9 | Hypothesis tests [3.0s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [0.7s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 1386.7 s
+Duration: 114.8 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)