[BioC] pre-ranked GSEA within R: options?

[Daniel Schmolze]

I want to do a GSEA entirely from within R, using genes ranked by my
own metric. At the moment I'm saving my ranked genes to a .rnk file,
then calling Broad's GSEA java program, then reading the resulting
output back into R (all I care about are the p-values in
gsea_report_for_na_pos_####.xls and gsea_report_for_na_neg_####.xls).
Cumbersome to say the least.

As far as I can tell, the Broad GSEA R script won't accept pre-ranked
genes, but maybe I'm wrong? If not, I'm interested in other options.
I'd like to specifically stick with the Broad GSEA algorithm if
possible.