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

1 files changed, 12 insertions, 12 deletions

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)