# HG changeset patch
# User testtool
# Date 1486653184 18000
# Node ID a266a7c268e98ca38e213e80582c2466cf19785c
# Parent  0262f5edecb93b7c5d52fed10f5bb4dbb3e13f2c
Uploaded

diff -r 0262f5edecb9 -r a266a7c268e9 GEO/getGEO.R
--- a/GEO/getGEO.R	Thu Feb 09 09:56:43 2017 -0500
+++ b/GEO/getGEO.R	Thu Feb 09 10:13:04 2017 -0500
@@ -4,7 +4,7 @@
 require("rtracklayer", quietly = TRUE)
 require("FDb.InfiniumMethylation.hg19", quietly = TRUE)
 
-options(warn = -1,"download.file.method"="wget")
+options("download.file.method"="wget")
 
 args <- commandArgs(trailingOnly = TRUE)
 GSMTable = args[1]
diff -r 0262f5edecb9 -r a266a7c268e9 GEO/getGEO.xml
--- a/GEO/getGEO.xml	Thu Feb 09 09:56:43 2017 -0500
+++ b/GEO/getGEO.xml	Thu Feb 09 10:13:04 2017 -0500
@@ -3,6 +3,9 @@
   <requirements>
          <requirement type="package" version="3.2.1">R</requirement>
      </requirements>
+     <stdio>
+         <exit_code range="1:"></exit_code>
+     </stdio>
   <command> Rscript $__tool_directory__/getGEO.R "$GSMTable" "$MetaTable" "$IlmnTable" "$gmTable"</command>
   <inputs>
     <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GEO table of data." label="[required] GSMTable">