From 027843d7913aa2fc58bfcd3f6604d6caf42bfe1c Mon Sep 17 00:00:00 2001
From: Lechu <alpof@yahoo.com>
Date: Sun, 4 Mar 2012 03:32:30 +0100
Subject: [PATCH] I've simply added a "library(grid)" call at the beginning of
 the R script generation since R 2.14.2 doesn't seem to load the "grid"
 package as default. I haven't tested it on previous R versions (you may edit
 the R version comment to be more precise if desired), but I'm almost certain
 that this library call shouldn't do any harm on them.

Signed-off-by: Ryan Poplin <rpoplin@broadinstitute.org>
---
 .../gatk/walkers/variantrecalibration/VariantRecalibrator.java  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 7cc5b1625..3cdcf4982 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -372,6 +372,8 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         stream.println("library(ggplot2)");
         // For compactPDF in R 2.13+
         stream.println("library(tools)");
+        // For graphical functions R 2.14.2+
+        stream.println("library(grid)");
 
         createArrangeFunction( stream );