diff --git a/R/checkForGitbook.R b/R/checkForGitbook.R
index 80c6744..cfe6927 100644
--- a/R/checkForGitbook.R
+++ b/R/checkForGitbook.R
@@ -6,7 +6,7 @@
 #' @param quiet logical indicating whether messages should be printed.
 #' @export
 checkForGitbook <- function(quiet=FALSE) {
-	if(system('npm', ignore.stdout=TRUE) != 0) {
+	if(system('npm -v', ignore.stdout=TRUE) != 0) {
 		stop("Cannot find node.js. You can install it from http://nodejs.org/download/")
 	}
 	if(system('gitbook', ignore.stdout=TRUE) != 0) {
diff --git a/R/gitbookInfo.R b/R/gitbookInfo.R
index 48a95c0..fbcc7b0 100644
--- a/R/gitbookInfo.R
+++ b/R/gitbookInfo.R
@@ -7,7 +7,11 @@
 #' @export
 gitbookInfo <- function() {
 	checkForGitbook(quiet=TRUE)
-	installed <- system('gitbook --version', intern=TRUE)
+	# Use npm instead of gitbook.
+  	listInstalledModules <- system("npm list -g", intern=TRUE);
+	gitbookIndex <- grep("gitbook@", listInstalledModules, fixed=TRUE);
+	position <- regexpr("gitbook@", listInstalledModules[gitbookIndex], fixed=TRUE);
+	installed <- substr( listInstalledModules[gitbookIndex], position+8, nchar(listInstalledModules[gitbookIndex]) );
 	current <- system('npm view gitbook version', intern=TRUE)
 	if(length(current) > 0) {
 		current <- current[1]
diff --git a/R/initGitbook.R b/R/initGitbook.R
index 4c6bd96..4023845 100644
--- a/R/initGitbook.R
+++ b/R/initGitbook.R
@@ -8,44 +8,41 @@
 #' 
 #' @export
 initGitbook <- function(dir=getwd()) {
-	dir <- normalizePath(dir)
-	checkForGitbook(quiet=TRUE)
-	oldwd <- setwd(dir)
-	test <- system(paste0('gitbook init ', dir))
-	if(test != 0) { stop("gitbook initalization failed") }
-	mdfiles <- list.files(dir, '*.md', recursive=TRUE, full.names=TRUE)
-	mdfiles <- mdfiles[-c(grep('README.md$', mdfiles),
-						  grep('SUMMARY.md$', mdfiles))]
-	mdfiles2 <- gsub('/.md$', '.Rmd', mdfiles)
-	file.rename(mdfiles, mdfiles2)
-	
-	knitr.header <- c( # TODO: make a package option?
-		"```{r knitsetup, echo=FALSE, results='hide', warning=FALSE, message=FALSE, cache=FALSE}",
-		"opts_knit$set(base.dir='./', fig.path='', out.format='md')",
-		"opts_chunk$set(prompt=TRUE, comment='', results='markup')",
-		"# See yihui.name/knitr/options for more Knitr options.",
-		"##### Put other setup R code here",
-		"",
-		"```",
-		""
-	)
-	for(rmd in mdfiles2) {
-		file <- file(rmd)
-		lines <- readLines(file)
-		close(file)
-		
-		#if the knitsetup block isn't already in the file, then add it
-		suppressWarnings(
-			if(grepl("r knitsetup.+\n", lines)) {
-				lines <- c(knitr.header, lines)
-			}
-		)
-		
-		file <- file(rmd)
-		writeLines(lines, file(rmd))
-		close(file)
-	}
-	
-	setwd(oldwd)
-	invisible()
+  dir <- normalizePath(dir)
+  checkForGitbook(quiet = TRUE)
+  oldwd <- setwd(dir)
+  test <- system(paste0("gitbook init ", dir))
+  if (test != 0) {
+    stop("gitbook initalization failed")
+  }
+  mdfiles <- list.files(dir, "*.md", recursive = TRUE, full.names = TRUE)
+  mdfiles <- mdfiles[-c(grep("README.md$", mdfiles), grep("SUMMARY.md$", mdfiles))]
+  mdfiles2 <- gsub("\\.md$", ".Rmd", mdfiles)
+  file.rename(mdfiles, mdfiles2)
+  knitr.header <- c("```{r knitsetup, echo=FALSE, results='hide', warning=FALSE, message=FALSE, cache=FALSE}", 
+                    "opts_knit$set(base.dir='./', fig.path='', out.format='md')", 
+                    "opts_chunk$set(prompt=TRUE, comment='', results='markup')", 
+                    "# See yihui.name/knitr/options for more Knitr options.", 
+                    "##### Put other setup R code here", "", "",
+                    "# end setup chunk",
+                    "```")
+  
+  for (rmd in mdfiles2) {
+    file <- file(rmd)
+    lines <- readLines(file)
+    close(file)
+    # don't inject knitr setup chunk if Rmd file 
+    # already has one, ie. editing an existing Rmd
+    # or the references Rmd, which has a different setup
+    toMatch <- c("r knitsetup", "r setup")
+    matches <- grepl(paste(toMatch,collapse="|"), lines)  
+    suppressWarnings(if (!any(matches)) {
+      lines <- c(knitr.header, lines)
+    })
+    file <- file(rmd)
+    writeLines(lines, file(rmd))
+    close(file)
+  }
+  setwd(oldwd)
+  invisible()
 }
diff --git a/R/publishGitbook.R b/R/publishGitbook.R
index d270220..6c487fd 100644
--- a/R/publishGitbook.R
+++ b/R/publishGitbook.R
@@ -14,16 +14,16 @@
 #' @export
 publishGitbook <- function(repo, 
 						   out.dir=paste0(getwd(), '/_book'),
-						   message='Update built gitbook') {
+						   msg='Update built gitbook') {
 	test <- system('git --version', ignore.stderr=TRUE, ignore.stdout=TRUE, show.output.on.console=FALSE)
 	if(test != 0) { stop('Git does not appear to be installed.')}
 	cmd <- paste0(
 		"cd ", out.dir, " \n",
 		"git init \n",
-		"git commit --allow-empty -m '", message,"' \n",
+		"git commit --allow-empty -m '", msg,"1' \n",
 		"git checkout -b gh-pages \n",
 		"git add . \n",
-		"git commit -am '", message, "' \n",
-		"git push git@github.com:", repo, " gh-pages --force ")
+		"git commit -a -m '", msg, "2' \n",
+		"git push https://github.com/", repo, " gh-pages --force ")
 	system(cmd)
 }