Guido Hooiveld

For me the analysis takes just few seconds.... Note the warnings on ties and duplicate entries. The warning on ties means that in `genelogFC` you have entries that have the...

To confirm: you copied/pasted my code above, and takes more than few seconds? Also, how long does the code take below that uses the included example data? Again, for me...

sorry, that was for the overrepresentation (ORA) function, not GSEA.... For KEGG-based GSEA it takes my computer ~14 seconds. ``` > library(clusterProfiler) > data(geneList, package="DOSE") > kkk > head(kkk) ID...

Well, there is not much anymore I can come up with... other than that the issue seems to be specific to your system. Sorry. Some last suggestions: Also reinstall `fgsea`...

Maybe you could try this on another computer, e.g. from a colleague? Anyway, please report back.

Happy to hear you found the culprit! Also thanks for reporting back since others may find this useful information when experiencing the same behavior.

Using` R-4.2.2` on my Windows machine I could reproduce your problem. That is, after an overnight the `gseGO` analysis wasn't finished, so I killed it. Interestingly, when I changed` minGSSize`...

I 'played' with your data set a little more, and I found that even when using up-to-date versions of `R` (and `clusterProfiler` / `fgsea`) with `minGSSize=10` `gseGO` (still!) hangs on...

Your code in the 2nd code box, starting from the line `kegg_genes

So if I understand you correctly, you would like to visualize the network of the top 5 most significant gene sets in a `cnetplot`, thereby using your preferred color scale...