error ssGSEA.ROC

[Hai Tran]

Hi everyone,

I was trying to compare ssGSEA results of two group phenotype. It came following error:

Error in library("getopt") : there is no package called ‘getopt’ Calls: suppressMessages -> withCallingHandlers Execution halted

My cls file is following:

 6 2 1                                                    

# I II                                                    
I    I    I    I    II    II

Somebody is familiar with this error? 

Thank you in advance!

Hai

[Anthony Castanza]

Hello Hai

It looks like there was an error in the construction of the back end of that module resulting in a missing dependency. We’ll get that fixed asap.

 

In the mean time, you might try running this version: https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:8080.gpserver.ip-172-31-26-71.ip-172-31-26-71.ec2.internal:genepatternmodules:177:1.0.1 the computations are the same but it uses a different, albeit slightly slower back end – but fortunately one that should avoid this issue.

 

-Anthony

 

Anthony S. Castanza, PhD

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Hai Tran]

Dear Anthony,

Thank you very much for your quick response and help. The version in clound you suggested has worked without any error.

Best,

Hai