Prepare release of v1.2.4v1.2.4

- Update DESCRIPTION
- Update Makefile to document how to use R-patched
- Remove markup from two URLs to avoid CRAN NOTE
- Switch two vignettes from html_document to html_vignette to save space
  in the docs directory, also avoiding a CRAN NOTE
- Complete rebuild of pkgdown docs for release

3 files changed, 23 insertions, 24 deletions

diff --git a/log/build.log b/log/build.log
index e077c30c..30c5e432 100644
--- a/log/build.log
+++ b/log/build.log
@@ -6,5 +6,5 @@
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
 Removed empty directory ‘mkin/vignettes/web_only’
-* building ‘mkin_1.2.3.tar.gz’
+* building ‘mkin_1.2.4.tar.gz’
 
diff --git a/log/check.log b/log/check.log
index b58119ef..970fbc7a 100644
--- a/log/check.log
+++ b/log/check.log
@@ -1,13 +1,17 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.2.3 (2023-03-15)
+* using R version 4.3.0 Patched (2023-05-18 r84448)
 * 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)
 * 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 ‘1.2.3’
+* this is package ‘mkin’ version ‘1.2.4’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
+* checking CRAN incoming feasibility ... [2s/10s] Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <johannes.ranke@jrwb.de>’
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -21,8 +25,7 @@ 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
@@ -59,7 +62,7 @@ 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 ... [10s/10s] OK
+* checking examples ... OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
@@ -71,9 +74,5 @@ unable to verify current time
 * 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 8166668a..b1b4ae31 100644
--- a/log/test.log
+++ b/log/test.log
@@ -8,22 +8,22 @@
 ✔ |        12 | Confidence intervals and p-values [0.4s]
 ✔ |     1  12 | Dimethenamid data from 2018 [12.5s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_dmta.R:88'): Different backends get consistent results for SFO-SFO3+, dimethenamid data
+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 [2.4s]
+✔ |        14 | Error model fitting [2.3s]
 ✔ |         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 [19.1s]
-✔ |     2  16 | Nonlinear mixed-effects models [148.6s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [18.9s]
+✔ |     2  16 | Nonlinear mixed-effects models [148.4s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_mixed.R:78'): saemix results are reproducible for biphasic fits
+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:131'): SFO-SFO saemix specific analytical solution work
+Skip ('test_mixed.R:133:3'): SFO-SFO saemix specific analytical solution work
 Reason: This is seldom used, so save some time
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
@@ -31,14 +31,14 @@ Reason: This is seldom used, so save some time
 ✔ |         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 [23.1s]
+✔ |        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 [3.9s]
-✔ |        15 | Plotting [4.4s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [3.5s]
+✔ |        15 | Plotting [4.5s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  36 | saemix parent models [31.1s]
+✔ |     1  36 | saemix parent models [30.7s]
 ────────────────────────────────────────────────────────────────────────────────
-Skip ('test_saemix_parent.R:143'): We can also use mkin solution methods for saem
+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]
@@ -51,7 +51,7 @@ 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: 260.5 s
+Duration: 259.6 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)