Could not run homoplasyFinder R

[hmamine]

Hello, I am trying to run homoplasyFinder (R) on set of whole genome multi-fasta alignment. The file have gaps. I run to the following error. If feedback on the wright way would be helpful.

> library(library(homoplasyFinder)
> fasta.file<-file.path("multi_ska_out.aln")
> tree.file<-file.path("Bbss_out_gbbins.final_tree.tre")
> inconsistentPositions <- runHomoplasyFinderInJava(treeFile=tree.file, fastaFile=fasta.file,  path="/home/mahassani/Biodata/Boston/v4/")
> Error in .jcheck() : AttachCurrentThread failed! (result:-1)