correct vignettes to pre-generate on CRAN

Author: TomKellyGenetics

.Rbuildignore

@@ -7,7 +7,6 @@
 ^CRAN-RELEASE$
 ^ISSUE_TEMPLATE.md$
 ^LICENSE$
-^Meta$
 ^\.Rproj\.user$
 ^\.circleci/config\.yml$
 ^\.travis\.yml$
@@ -33,11 +32,12 @@
 ^vignettes/*/*/*RData
 ^vignettes/*gif
 ^vignettes/cache$
-^vignettes/*html
 ^vignettes/import_reactome.Rmd$
 ^vignettes/figure
 ^vignettes/simulate_expression_files$
 ^vignettes/simulate_expression_cache/html/
+^vignettes/simulate_expression.md
+^vignettes/plot_directed.md
 pdf
 png
 sty
@@ -50,11 +50,3 @@ inst/doc/._.DS_Store
 inst/doc/._plots_directed.html
 inst/doc/._simulate_expression.html
 inst/doc/._vignettes.zip
-vignettes/.DS_Store
-vignettes/._.DS_Store
-plots_directed.html
-plots_directed.Rmd
-plots_directed.md
-simulate_expression.html
-simulate_expression.Rmd
-simulate_expression.md

DESCRIPTION

@@ -25,11 +25,12 @@ Suggests:
     knitr (>= 1.5),
     markdown,
     prettydoc,
+    R.rsp,
     rmarkdown,
     testthat,
     scales,
     vdiffr
 LazyData: TRUE
 RoxygenNote: 7.1.1
 Encoding: UTF-8
-VignetteBuilder: knitr
+VignetteBuilder: R.rsp

vignettes/plots_directed.Rmd

@@ -16,7 +16,7 @@ output:
 toc-title: "Table of Contents"
 vignette: >
   %\VignetteIndexEntry{Directed plots for igraph objects}
-  %\VignetteEngine{knitr::knitr}
+  %\VignetteEngine{R.rsp::asis}
   %\VignetteEncoding{UTF-8}
 ---
 

vignettes/plots_directed.html

@@ -0,0 +1,3 @@
+%\VignetteIndexEntry{Directed plots for igraph objects}
+%\VignetteEngine{R.rsp::asis}
+%\VignetteEncoding{UTF-8}

vignettes/plots_directed.html.asis

@@ -3,20 +3,21 @@ title: "graphsim: simulating continuous data based on network graph structures"
 author: "S. Thomas Kelly^1,2^, Michael A. Black^1^ <br> ^1^ Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand <br> ^2^ RIKEN Center for Integrative Medical Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama"
 date: "`r  format(Sys.time(), '%A %d %B %Y')`"
 output:
-  prettydoc::html_pretty:
-       theme: cayman
-  #html_document:
+    html_document
+#  prettydoc::html_pretty:
+#  #     theme: cayman
+#  html_document
        #theme: united
-       number_sections: true
-       toc: true
-       toc_depth: 4
+       #number_sections: true
+       #toc: true
+       #toc_depth: 4
        #toc_float: true
        #code_folding: show
-       keep_html: true
-toc-title: "Table of Contents"
+       #keep_html: true
+#toc-title: "Table of Contents"
 vignette: >
   %\VignetteIndexEntry{Simulating network graph structure in continuous data}
-  %\VignetteEngine{knitr::knitr}
+  %\VignetteEngine{R.rsp::asis}
   %\VignetteEncoding{UTF-8}
 ---
 

vignettes/simulate_expression.Rmd

@@ -0,0 +1,3 @@
+%\VignetteIndexEntry{Simulating network graph structure in continuous data}
+%\VignetteEngine{R.rsp::asis}
+%\VignetteEncoding{UTF-8}