From 7ab05064a1f784e0288869d5cd7bd151bc739946 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 13 Feb 2023 20:13:56 +0100
Subject: Prepare to keep prebuilt vignettes as pdf in git

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 5bec45e6..6cf7f403 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,4 +31,3 @@ vignettes/*_files/
 vignettes/prebuilt/*_cache
 vignettes/prebuilt/*_files
 vignettes/prebuilt/*_dlls
-vignettes/prebuilt/*.pdf
-- 
cgit v1.2.1


From 9b5a04b645235b10fe574eb14f3e7c6717c43b5a Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 13 Feb 2023 21:20:38 +0100
Subject: Update mmkin docs, parallel is not loaded any more

---
 R/mmkin.R | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/R/mmkin.R b/R/mmkin.R
index 01e53290..e1537685 100644
--- a/R/mmkin.R
+++ b/R/mmkin.R
@@ -62,16 +62,15 @@
 #' # allow to plot the observed variables separately
 #' plot(fits.0[1, 1])
 #'
-#' # On Windows, we can use multiple cores by making a cluster using the parallel
-#' # package, which gets loaded with mkin, and passing it to mmkin, e.g.
-#' cl <- makePSOCKcluster(12)
+#' # On Windows, we can use multiple cores by making a cluster first
+#' cl <- parallel::makePSOCKcluster(12)
 #' f <- mmkin(c("SFO", "FOMC", "DFOP"),
 #'   list(A = FOCUS_2006_A, B = FOCUS_2006_B, C = FOCUS_2006_C, D = FOCUS_2006_D),
 #'   cluster = cl, quiet = TRUE)
 #' print(f)
 #' # We get false convergence for the FOMC fit to FOCUS_2006_A because this
 #' # dataset is really SFO, and the FOMC fit is overparameterised
-#' stopCluster(cl)
+#' parallel::stopCluster(cl)
 #' }
 #'
 #' @export mmkin
-- 
cgit v1.2.1


From c7cc91c47f9b074521fcaaa05a020525d719c2d9 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 17 Feb 2023 08:19:46 +0100
Subject: Fix path, build target for prebuilt pdf vignettes

---
 GNUmakefile                             | 3 +++
 vignettes/dmta_parent_2022_prebuilt.rnw | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/GNUmakefile b/GNUmakefile
index 9f268335..42df55d5 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -99,6 +99,9 @@ testcheck: roxygen test check
 README.html: README.md
 	"$(RBIN)/Rscript" -e "rmarkdown::render('README.md', output_format = 'html_document', output_options = list(mathjax = NULL))"
 
+vignettes/%.pdf: vignettes/references.bib vignettes/%.rnw
+	"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.rnw', dir = 'vignettes')"
+
 vignettes/%.html: vignettes/mkin_vignettes.css vignettes/references.bib vignettes/%.rmd
 	"$(RBIN)/Rscript" -e "tools::buildVignette(file = 'vignettes/$*.rmd', dir = 'vignettes')"
 
diff --git a/vignettes/dmta_parent_2022_prebuilt.rnw b/vignettes/dmta_parent_2022_prebuilt.rnw
index cbfa6897..6267bffc 100644
--- a/vignettes/dmta_parent_2022_prebuilt.rnw
+++ b/vignettes/dmta_parent_2022_prebuilt.rnw
@@ -3,5 +3,5 @@
 %\VignetteIndexEntry{Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P}
 
 \begin{document}
-\includepdf[pages=-, fitpaper=true]{2022_wp_1/2022_dmta_parent.pdf}
+\includepdf[pages=-, fitpaper=true]{prebuilt/2022_dmta_parent.pdf}
 \end{document}
-- 
cgit v1.2.1