Debug library dependancies

bin/GOEnrichment.R

@@ -15,12 +15,13 @@
 packages <- c("optparse", # to read arguments from a command line
               "ggplot2", # nice plots
               "RJSONIO", # work with JSON file
-              "DBI")
+              "DBI",
+		"svglite")
 
 for(package in packages){
   # if package is installed locally, load
   if (!(package %in% rownames(installed.packages()))) {
-    install.packages(package)
+    install.packages(package, repos="http://cran.univ-paris1.fr")
   }
   do.call('library', list(package))
 }
@@ -29,6 +30,8 @@ for(package in packages){
 if (!("topGO" %in% rownames(installed.packages()))) {
   source("http://www.bioconductor.org/biocLite.R")
   biocLite("topGO", suppressUpdates = TRUE, suppressAutoUpdate = TRUE, ask = FALSE)
+
+  biocLite("Rgraphviz", suppressUpdates = TRUE, suppressAutoUpdate = TRUE, ask = FALSE)
 }
 library(topGO) # GO enrichment