[svtoolkit-help] SVDiscovery error for installation test

[Ashish K. <as...@we...>]

Hi Bob,

While running the installation test, it seems that the SVDiscovery step complains about an R function. I have the "coin package" is installed on my server.
I am pasting the error below, please advice.
Best,
Ashish


##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.RuntimeException: Error running script /ib/users/ashish/genostrip/svtoolkit/R/discovery/compute_ranksum_pvalue.R: Error in function (classes, fdef, mtable)  :
  unable to find an inherited method for function "pvalue", for signature "htest"
Calls: main ... compute.ranksum.pvalue.coin -> pvalue -> <Anonymous>
Execution halted

        at org.broadinstitute.sv.discovery.ClusterDepthModule.computeRankSumPValue(ClusterDepthModule.java:284)
        at org.broadinstitute.sv.discovery.ClusterDepthModule.computeDepth(ClusterDepthModule.java:195)
        at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processCluster(DeletionDiscoveryAlgorithm.java:395)
        at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.processClusters(DeletionDiscoveryAlgorithm.java:303)
        at org.broadinstitute.sv.discovery.DeletionDiscoveryAlgorithm.runDiscovery(DeletionDiscoveryAlgorithm.java:163)
        at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:150)
        at org.broadinstitute.sv.discovery.SVDiscoveryWalker.onTraversalDone(SVDiscoveryWalker.java:43)
        at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129)
        at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:75)
        at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:217)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:111)
        at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:110)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:239)
        at org.broadinstitute.sv.main.SVCommandLine.main(SVCommandLine.java:72)
        at org.broadinstitute.sv.main.SVDiscovery.main(SVDiscovery.java:21)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.0.5039M):