Update docs, check and test on RStudio server

5 files changed, 49 insertions, 56 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 ]
diff --git a/man/read_spreadsheet.Rd b/man/read_spreadsheet.Rd
index 41c32108..eefda692 100644
--- a/man/read_spreadsheet.Rd
+++ b/man/read_spreadsheet.Rd
@@ -36,7 +36,7 @@ The first row read after the header read in from this sheet is assumed
 to contain name and acronym of the parent compound.
 
 The dataset sheets should be named using the dataset numbers read in from
-the 'Datasets' sheet, i.e. '1', '2', ... . In each dataset sheet, name
+the 'Datasets' sheet, i.e. '1', '2', ... . In each dataset sheet, the name
 of the observed variable (e.g. the acronym of the parent compound or
 one of its transformation products) should be in the first column,
 the time values should be in the second colum, and the observed value
@@ -50,6 +50,6 @@ column and the column must have the same name as the second column in
 Their names should preferably not contain special characters like spaces,
 so they can be easily used for specifying covariate models.
 
-An similar data structure is defined as the R6 class \link{mkindsg}, but
+A similar data structure is defined as the R6 class \link{mkindsg}, but
 is probably more complicated to use.
 }
diff --git a/mkin.Rproj b/mkin.Rproj
index fac143c3..beb8549b 100644
--- a/mkin.Rproj
+++ b/mkin.Rproj
@@ -19,4 +19,7 @@ BuildType: Makefile
 
 UseNativePipeOperator: Yes
 
+MarkdownWrap: Column
+MarkdownWrapAtColumn: 80
+
 SpellingDictionary: en_GB