I try to run the example of fgsea package with R version 4.0.2 :

data(examplePathways)
data(exampleRanks)
typeof(examplePathways)
fgseaRes <- fgsea(pathways = examplePathways, 
                  stats = exampleRanks,
                  minSize=15,
                  maxSize=500,
                  nperm=10000)

I got this warning and I don't know how to deal with that

Warning messages:
1: In fgsea(pathways = examplePathways, stats = exampleRanks, minSize = 15,  :
  You are trying to run fgseaSimple. It is recommended to use fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument in the fgsea function call.
2: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
3: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
4: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
5: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
6: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement
7: In serialize(data, node$con) :
  'package:stats' peut-être indisponible lors du chargement

I use this to install the package :

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("fgsea")

There are two warnings.

You are trying to run fgseaSimple can be solved by removing nperm parameter at all. The nperm parameter is deprecated, and generally shouldn't be used. Also, where this example is coming from?

The second warning about serialize(data, node$con) is related to parallel execution. Not sure what exactly happens, but a workaround is to run fgsea in single-threaded mode, for example by specifying nproc=1 as a parameter.

Thank you for your help ! I did this and it is work well !

data(examplePathways)
data(exampleRanks)
typeof(examplePathways)
fgseaRes <- fgsea(pathways = examplePathways, 
                  stats = exampleRanks,
                  minSize=15,
                  maxSize=500,
                  nproc=1, 
                  eps = 0)

I foun this example here : https://bioconductor.org/packages/release/bioc/vignettes/fgsea/inst/doc/fgsea-tutorial.html