Merge pull request #169 from jsta/patch-1

[rnaseq-cwl-training.git] / bin / generate_md_episodes.R

diff --git a/bin/generate_md_episodes.R b/bin/generate_md_episodes.R
index 43bf65e118eea26b7900b3fd1a31d8ec2170ffd2..4ea9835037a81c7e9c657681b12c46cfa30b235f 100644 (file)
--- a/bin/generate_md_episodes.R
+++ b/bin/generate_md_episodes.R
@@ -1,15 +1,30 @@
 generate_md_episodes <- function() {
 
-    if (require("knitr")) {
-        if (packageVersion("knitr") < '1.9.19') {
-            stop("knitr must be version 1.9.20 or higher")
-        }
-    } else stop("knitr 1.9.20 or above is needed to build the lessons.")
+    library("methods")
+    
+    if (require("knitr") && packageVersion("knitr") < '1.9.19')
+        stop("knitr must be version 1.9.20 or higher")
 
     if (!require("stringr"))
         stop("The package stringr is required for generating the lessons.")
 
-    ## find all the Rmd files, and generates the paths for their respective outputs
+    if (require("checkpoint") && packageVersion("checkpoint") >=  '0.4.0') {
+        required_pkgs <-
+             checkpoint:::scanForPackages(project = "_episodes_rmd",
+                                          verbose=FALSE, use.knitr = TRUE)$pkgs
+    } else {
+        stop("The checkpoint package (>= 0.4.0) is required to build the lessons.")
+    }
+
+    missing_pkgs <- required_pkgs[!(required_pkgs %in% rownames(installed.packages()))]
+
+    if (length(missing_pkgs)) {
+        message("Installing missing required packages: ",
+                paste(missing_pkgs, collapse=", "))
+        install.packages(missing_pkgs)
+    }
+
+    ## find all the Rmd files, and generate the paths for their respective outputs
     src_rmd <- list.files(pattern = "??-*.Rmd$", path = "_episodes_rmd", full.names = TRUE)
     dest_md <- file.path("_episodes", gsub("Rmd$", "md", basename(src_rmd)))