--- a/GRsetFromGEO/GRsetFromGEO.R	Mon Apr 24 10:09:39 2017 -0400
+++ b/GRsetFromGEO/GRsetFromGEO.R	Mon Apr 24 10:31:20 2017 -0400
@@ -1,9 +1,10 @@
-require("BiocGenerics", quietly = TRUE)
-require("data.table", quietly = TRUE)
 require("GEOquery", quietly = TRUE)
 require("minfi", quietly = TRUE)
 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
 
+options(warn = -1)
+options("download.file.method"="wget")
+
 args <- commandArgs(trailingOnly = TRUE)
 GSE = args[1] 
 output = args[2] 
@@ -26,7 +27,13 @@
 mergeManifest = FALSE
 i = 1
 
-gset <- GEOquery::getGEO(GSE)
+gset <- getGEO(GSE)
+
+if (is.null(GSE)) {
+  stop("Must specify GSE")
+} else {
+  options(download.file.method.GEOquery = "wget")}
+  
 gset <- gset[[1]]
 
 platform <- annotation(gset)