AnalyzeCovariates Plots Debug

 I didn't instal the packages of, ggplots, gplots, reshape, gsalib... etc that cause the problem.

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##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
org.broadinstitute.gatk.utils.R.RScriptExecutorException: RScript exited with 1
at org.broadinstitute.gatk.utils.R.RScriptExecutor.exec(RScriptExecutor.java:174)
at org.broadinstitute.gatk.utils.recalibration.RecalUtils.generatePlots(RecalUtils.java:576)
at org.broadinstitute.gatk.tools.walkers.bqsr.AnalyzeCovariates.generatePlots(AnalyzeCovariates.java:380)
at org.broadinstitute.gatk.tools.walkers.bqsr.AnalyzeCovariates.initialize(AnalyzeCovariates.java:394)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
##### ERROR
##### ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
##### ERROR If not, please post the error message, with stack trace, to the GATK forum.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: RScript exited with 1