Update docs, check and test on RStudio server

3 files changed, 44 insertions, 54 deletions

diff --git a/log/build.log b/log/build.log
index 717128fd..11086361 100644
--- a/log/build.log
+++ b/log/build.log
@@ -7,4 +7,6 @@
 * checking for empty or unneeded directories
 Removed empty directory ‘mkin/vignettes/web_only’
 * building ‘mkin_1.2.5.tar.gz’
+Warning: invalid uid value replaced by that for user 'nobody'
+Warning: invalid gid value replaced by that for user 'nobody'
 
diff --git a/log/check.log b/log/check.log
index fedb0bd9..64457e57 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,17 +1,17 @@
-* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
+* using log directory ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck’
 * using R version 4.3.1 (2023-06-16)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
-    gcc (Debian 12.2.0-14) 12.2.0
-    GNU Fortran (Debian 12.2.0-14) 12.2.0
-* running under: Debian GNU/Linux 12 (bookworm)
+    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.3 LTS
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
 * this is package ‘mkin’ version ‘1.2.5’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... [3s/12s] Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... [5s/26s] Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -45,7 +45,7 @@ Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [15s/15s] OK
+* checking R code for possible problems ... [14s/15s] OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -62,22 +62,22 @@ 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 ... [18s/18s] OK
+* checking examples ... [20s/22s] 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 ... [17s/17s] OK
+* checking re-building of vignette outputs ... [17s/18s] OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... NOTE
-Skipping checking math rendering: package 'V8' unavailable
+Skipping checking HTML validation: no command 'tidy' found
 * 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’
+  ‘/home/agsad.admin.ch/f80868656/projects/mkin/mkin.Rcheck/00check.log’
 for details.
 
 
diff --git a/log/test.log b/log/test.log
index 2f1b6949..3bca2e6a 100644
--- a/log/test.log
+++ b/log/test.log
@@ -4,59 +4,47 @@
 ✔ |         5 | Analytical solutions for coupled models [2.9s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
-✔ |         6 | Use of precompiled symbols in mkinpredict [5.7s]
-✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [33.1s]
-────────────────────────────────────────────────────────────────────────────────
-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 15 minutes on my system
-────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [7.5s]
+✔ |         6 | Use of precompiled symbols in mkinpredict [6.6s]
+✔ |        12 | Confidence intervals and p-values [1.1s]
+✔ |     1  12 | Dimethenamid data from 2018 [32.2s]
+✔ |        14 | Error model fitting [5.4s]
 ✔ |         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 [43.6s]
-✔ |     2  16 | Nonlinear mixed-effects models [364.4s]
-────────────────────────────────────────────────────────────────────────────────
-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
-────────────────────────────────────────────────────────────────────────────────
+✔ |         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 [46.9s]
+✔ |     2  16 | Nonlinear mixed-effects models [399.6s]
 ✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        10 | Special cases of mkinfit calls [0.4s]
-✔ |         3 | mkinfit features [0.7s]
-✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |        12 | Multistart method for saem.mmkin models [80.2s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.0s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [9.1s]
+✔ |        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 [50.1s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.8s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [9.3s]
 ✔ |        15 | Plotting [10.9s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [77.0s]
-────────────────────────────────────────────────────────────────────────────────
-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
-────────────────────────────────────────────────────────────────────────────────
+✔ |     1  36 | saemix parent models [68.4s]
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.2s]
 ✔ |        11 | Processing of residue series
-✔ |        10 | Fitting the SFORB model [3.5s]
+✔ |        10 | Fitting the SFORB model [3.8s]
 ✔ |         1 | Summaries of old mkinfit objects
-✔ |         5 | Summary [0.2s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.8s]
-✔ |         9 | Hypothesis tests [6.7s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.0s]
+✔ |         5 | Summary
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [1.9s]
+✔ |         9 | Hypothesis tests [6.4s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [1.4s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 656.7 s
+Duration: 655.6 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 is seldom used, so save some time (1)
-• This still takes almost 2.5 minutes although we do not solve ODEs (1)
+── 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'
 
 [ FAIL 0 | WARN 0 | SKIP 4 | PASS 281 ]