Closure subsetting error

[Sellerzzz]

Hi,

First off, thank you very much for porting the GSEA workflow to R, very useful tool.

I am having an issue that I have not ran across before after using the package successfully for ~2months.

This error "Error in V[, 1] : object of type 'closure' is not subsettable" pops up after a 'successful' analysis (p values are produced along with tables and most of the plots). I think this may have something to do with the $report1 and $report2 printing.

I will attach the files I am using for the GSEA, can you try to reproduce the error?
I have renamed the files all to .txt so that Github will let me attach.

command:
GSEA(input.ds = "GSEA/combi_acc.gct", input.cls = "GSEA/combi_acc.cls",
gs.db = "ISG_EB.gmt", output.directory = "test_GSEA", doc.string = "TEST", save.intermediate.results = T)

BW,
Rob

ISG_EB.txt
combi_acc_cls.txt
combi_acc_gct.txt

[ACastanza]

Hi Rob,

I glanced at your input, it looks like you only have one gene set in your GMT? That might be causing the error with subsetting the report. We never tested this with only one input set. I'll try running some test runs, but you might try changing out the GMT to one of the MSigDB gmts with the same data otherwise and see if it still gives the error in case you get an opportunity to look into it before I do.

-Anthony