Merge remote-tracking branch 'refs/remotes/origin/main'

3 files changed, 23 insertions, 22 deletions

diff --git a/log/build.log b/log/build.log
index c2001830..de7e4488 100644
--- a/log/build.log
+++ b/log/build.log
@@ -7,5 +7,5 @@
 * checking for empty or unneeded directories
 Removed empty directory ‘mkin/inst/rmarkdown/templates/hierarchical_kinetics_parent’
 Removed empty directory ‘mkin/vignettes/web_only’
-* building ‘mkin_1.2.8.tar.gz’
+* building ‘mkin_1.2.9.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index 5e777a87..58615282 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,6 +1,6 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.3.2 (2023-10-31)
-* using platform: x86_64-pc-linux-gnu (64-bit)
+* using R version 4.4.0 (2024-04-24)
+* using platform: x86_64-pc-linux-gnu
 * R was compiled by
     gcc (Debian 12.2.0-14) 12.2.0
     GNU Fortran (Debian 12.2.0-14) 12.2.0
@@ -9,9 +9,9 @@
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘1.2.8’
+* this is package ‘mkin’ version ‘1.2.9’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... [2s/14s] Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -32,7 +32,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking for left-over files ... OK
 * checking index information ... OK
 * checking package subdirectories ... OK
-* checking R files for non-ASCII characters ... OK
+* checking code files for non-ASCII characters ... OK
 * checking R files for syntax errors ... OK
 * checking whether the package can be loaded ... OK
 * checking whether the package can be loaded with stated dependencies ... OK
@@ -62,11 +62,11 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking sizes of PDF files under ‘inst/doc’ ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... OK
+* checking examples ... [10s/10s] 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 package vignettes ... OK
 * checking re-building of vignette outputs ... OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
diff --git a/log/test.log b/log/test.log
index 9dc63675..e92a7409 100644
--- a/log/test.log
+++ b/log/test.log
@@ -4,39 +4,40 @@
 ✔ |          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 [3.2s]
+✔ |          6 | Use of precompiled symbols in mkinpredict [3.1s]
 ✔ |         12 | Confidence intervals and p-values
-✔ |      1  12 | Dimethenamid data from 2018 [13.8s]
-✔ |         14 | Error model fitting [2.5s]
+✔ |      1  12 | Dimethenamid data from 2018 [13.0s]
+✔ |         14 | Error model fitting [2.6s]
 ✔ |          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 [19.8s]
-✔ |      2  16 | Nonlinear mixed-effects models [149.6s]
+✔ |         10 | Batch fitting and diagnosing hierarchical kinetic models [19.7s]
+✔ |      2  16 | Nonlinear mixed-effects models [144.7s]
 ✔ |          3 | Test dataset classes mkinds and mkindsg
 ✔ |         10 | Special cases of mkinfit calls
 ✔ |          3 | mkinfit features
 ✔ |          8 | mkinmod model generation and printing
 ✔ |          3 | Model predictions with mkinpredict
-✔ |         12 | Multistart method for saem.mmkin models [23.6s]
-✔ |         16 | Evaluations according to 2015 NAFTA guidance [1.6s]
-✔ |          9 | Nonlinear mixed-effects models with nlme [4.0s]
-✔ |         15 | Plotting [4.7s]
+✔ |         12 | Multistart method for saem.mmkin models [23.3s]
+✔ |         16 | Evaluations according to 2015 NAFTA guidance [1.5s]
+✔ |          9 | Nonlinear mixed-effects models with nlme [3.7s]
+✔ |         15 | Plotting [4.5s]
 ✔ |          4 | Residuals extracted from mkinfit models
-✔ |      1  38 | saemix parent models [36.4s]
+✔ |      1  38 | saemix parent models [34.8s]
 ✔ |          2 | Complex test case from Schaefer et al. (2007) Piacenza paper
 ✔ |         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)
-✔ |          9 | Hypothesis tests [3.1s]
+✔ |          9 | Hypothesis tests [2.9s]
 ✔ |          4 | Calculation of maximum time weighted average concentrations (TWAs)
+✔ |          2 | water-sediment
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 270.7 s
+Duration: 262.3 s
 
 ── Skipped tests (4) ───────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 5 minutes on my new system
@@ -47,4 +48,4 @@ Duration: 270.7 s
 • This still takes almost 2.5 minutes although we do not solve ODEs (1):
   'test_saemix_parent.R:143:3'
 
-[ FAIL 0 | WARN 0 | SKIP 4 | PASS 283 ]
+[ FAIL 0 | WARN 0 | SKIP 4 | PASS 285 ]