I try to run an fgsea analyses. So I create my own database looks like this :

df_db <- read.csv('pathway_ecnumber.csv',sep=",")

df_db
path:map00010  3.2.1.86
path:map00500  3.2.1.86
path:map00010   4.1.1.1
path:map01100   4.1.1.1
path:map01110   4.1.1.1
path:map01130   4.1.1.1
path:map00010  4.1.1.32
path:map00020  4.1.1.32
path:map00620  4.1.1.32
path:map01100  4.1.1.32
path:map01110  4.1.1.32

df_db$enzyme<-gsub("ec:","",df_db$enzyme)
db_final<-df_db %>% dlply( "pathway", `[[`, "enzyme" ) %>% c
database_pathway <- db_final[!duplicated(names(db_final))]

database_pathway

$`path:map05410`
[1] "2.7.11.11" "3.4.15.1"  "2.7.11.1" 

$`path:map05414`
[1] "4.6.1.1"   "2.7.11.11" "2.7.11.1" 

$`path:map05416`
[1] "3.4.22.56" "3.4.22.61" "3.4.22.62" "2.7.10.2" 

And I create my rank like this :

   df_select <- df_data %>% dplyr::select(ECNUMBER, log2FoldChange)
    df_na <- df_select %>% drop_na()
    df_split <- df_na %>% mutate(ECNUMBER = strsplit(as.character(ECNUMBER), ",")) %>% unnest(ECNUMBER)
    df_split <- as.data.frame(df_split)
    df_unique <- unique(df_split)  
    df_na <- na.omit(df_unique)
    df1 <- filter(df_na, log2FoldChange != 0)
    geneList <- df1[,2]
    names(geneList) <- as.character(df1[,1])
    geneList2 = sort(geneList, decreasing = T)

geneList2
3.4.21.102   2.7.1.221    2.7.7.13     1.1.1.3    1.1.1.42   1.14.19.9 
      3.217       3.217       3.217       3.217       3.217       3.217

At the end I got two warnings, and I don't know how to deal with it :

Warning messages:
1: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are ties in the preranked stats (81.54% of the list).
The order of those tied genes will be arbitrary, which may produce unexpected results.
2: In preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam,  :
  There are duplicate gene names, fgsea may produce unexpected results.

The second warning I try to resolve with this line but it is not working :

df_database <- database_pathway[!duplicated(names(database_pathway))]

I believe you should think over your design, as these warnings illustrate the problems in it.

It is very suspicious that you have multiple EC entries having exact same log2FC. This is either an error, or a flaw in the design, as the same gene can have multiple enzyme functions and single gene logFC goes to multiple EC numbers. However, GSEA assumes independence of the gene ranks, as it tests whether gene set looks randomly selected or not.

For the second warning, similarly, I expect you have a single enzyme can be represented by multiple genes, so you have multiple entries with the same EC number, which triggers the second warning.