Re: [svtoolkit-help] SVDiscovery error for installation test

[Bob H. <han...@br...>]

Hi, Ashish,
I don't know the exact problem, but it seems like something with your R 
environment.
You can try running the following short R script:

require("coin")
df = data.frame(COVERAGE=1:10)
df$DELETED = as.factor(df$COVERAGE > 5)
wilcox_test(COVERAGE ~ DELETED, df, alternative="l")

which will hopefully reproduce the problem so that you can diagnose it.
Something approximating this isn't running when R is invoked from java.

-Bob

On 9/8/11 3:05 PM, Ashish Kumar wrote:
>
> 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):
>
>
>
> ------------------------------------------------------------------------------
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