Try upgrading jekyll

Gemfile

@@ -1,3 +1,3 @@
 source 'https://rubygems.org'
 gem 'mime-types'
-gem 'jekyll', '~>2.5.3'
+gem 'jekyll', '~>3.1'

Gemfile.lock

@@ -1,69 +1,41 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    blankslate (2.1.2.4)
-    classifier-reborn (2.0.4)
-      fast-stemmer (~> 1.0)
-    coffee-script (2.4.1)
-      coffee-script-source
-      execjs
-    coffee-script-source (1.9.1.1)
     colorator (0.1)
-    execjs (2.6.0)
-    fast-stemmer (1.0.2)
     ffi (1.9.10)
-    jekyll (2.5.3)
-      classifier-reborn (~> 2.0)
+    jekyll (3.1.1)
       colorator (~> 0.1)
-      jekyll-coffeescript (~> 1.0)
-      jekyll-gist (~> 1.0)
-      jekyll-paginate (~> 1.0)
       jekyll-sass-converter (~> 1.0)
       jekyll-watch (~> 1.1)
       kramdown (~> 1.3)
-      liquid (~> 2.6.1)
+      liquid (~> 3.0)
       mercenary (~> 0.3.3)
-      pygments.rb (~> 0.6.0)
-      redcarpet (~> 3.1)
+      rouge (~> 1.7)
       safe_yaml (~> 1.0)
-      toml (~> 0.1.0)
-    jekyll-coffeescript (1.0.1)
-      coffee-script (~> 2.2)
-    jekyll-gist (1.3.5)
-    jekyll-paginate (1.1.0)
-    jekyll-sass-converter (1.3.0)
-      sass (~> 3.2)
-    jekyll-watch (1.3.0)
+    jekyll-sass-converter (1.4.0)
+      sass (~> 3.4)
+    jekyll-watch (1.3.1)
       listen (~> 3.0)
     kramdown (1.9.0)
-    liquid (2.6.3)
-    listen (3.0.4)
+    liquid (3.0.6)
+    listen (3.0.6)
       rb-fsevent (>= 0.9.3)
-      rb-inotify (>= 0.9)
+      rb-inotify (>= 0.9.7)
     mercenary (0.3.5)
     mime-types (2.6.2)
-    parslet (1.5.0)
-      blankslate (~> 2.0)
-    posix-spawn (0.3.11)
-    pygments.rb (0.6.3)
-      posix-spawn (~> 0.3.6)
-      yajl-ruby (~> 1.2.0)
-    rb-fsevent (0.9.6)
-    rb-inotify (0.9.5)
+    rb-fsevent (0.9.7)
+    rb-inotify (0.9.7)
       ffi (>= 0.5.0)
-    redcarpet (3.3.3)
+    rouge (1.10.1)
     safe_yaml (1.0.4)
-    sass (3.4.19)
-    toml (0.1.2)
-      parslet (~> 1.5.0)
-    yajl-ruby (1.2.1)
+    sass (3.4.21)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  jekyll (~> 2.5.3)
+  jekyll (~> 3.1)
   mime-types
 
 BUNDLED WITH
-   1.10.6
+   1.11.2

_config.yml

@@ -1,5 +1,3 @@
 name: R for data science
-markdown: redcarpet
-highlighter: pygments
 
 exclude: ["CONTRIBUTING.md", "README.md", "book", "vendor"]

_plugins/rmarkdown.rb

@@ -20,7 +20,7 @@ module Jekyll
       f.flush
 
       # http://rubyquicktips.com/post/5862861056/execute-shell-commands
-      content = `cd _plugins && ./knit.r ../temp.Rmd`
+      content = `_plugins/knit.r temp.Rmd`
 
       if $?.exitstatus != 0
         raise "Knitting failed"

functions.Rmd

@@ -682,7 +682,7 @@ Think about a data frame as a list of columns (we'll make this definition precis
 
 That makes our for loop quite simple:
 
-```{r}
+```{r, eval = FALSE}
 for (i in seq_along(df)) {
   df[[i]] <- rescale01(df[[i]])
 }
@@ -690,7 +690,7 @@ for (i in seq_along(df)) {
 
 For loops are not as important in R as they are in other languages as rather than writing your own for loops, you'll typically use prewritten functions that wrap up common for-loop patterns. You'll learn about those in the next chapter.  These functions are important because they wrap up the book-keeping code related to the for loop, focussing purely on what's happening. For example the two for-loops we wrote above can be rewritten as:
 
-```{r}
+```{r, eval = FALSE}
 library(purrr)
 
 map_dbl(df, median)

www/.gitignore

@@ -1 +1,5 @@
 bootstrap-2.3.2
+bootstrap-3.3.5
+htmlwidgets-0.5.2
+jquery-1.11.3
+navigation-1.0