I’ve downloaded the library from Bioconductor directly using the biocLite command and am currently running it in R version 3.3.3 “Another Canoe.”
When running the fgsea command the algorithm runs quickly (less than 1 second) for any number of permutations less than 1000, only taking 1.46 seconds to run when nperm=1000. I am examining 5,858 gene sets with 1,269 ranked genes and receiving reasonable results. However, the algorithm does not complete when running with more than 1000 permutations. I first tried to run 10,000 permutations and the command never completed, then found that even trying to run it with 1001 permutations results in the command running in an infinite loop.
How would you recommend proceeding?