error when running processVCF()

[vojtechhuser]

btw. I had to install one dependency separately but after then loading worked.

My code is below.
I am using a project from synapse with some VCF data.

#install.packages("devtools")
devtools::install_github("odyOSG/KOIOS")

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

BiocManager::install("GenomeInfoDb")

#install.packages('GenomeInfoDb')

m=read_delim(file.path(folder,'data_mutations_extended.txt'),skip=0)
names(m)

library(KOIOS)

#Load the OMOP Genomic Vocabulary into R
concepts <- loadConcepts()

#Specify input file or directort
vcf <- loadVCF(userVCF = "Input.vcf")

#Specify and load human reference genome, if known
ref <- "hg19"
ref.df <- loadReference(ref)

vcf=head(m,100)
#Process VCF and generate all relevant HGVSG identifiers for input records
vcf.df <- processVCF(vcf)

error

vcf.df <- processVCF(vcf)

Error in .setupMethodsTables(fdef, initialize = TRUE) :
no slot of name "group" for this object of class "derivedDefaultMethod"

columns

names(m)
[1] "Hugo_Symbol" "Entrez_Gene_Id" "Center" "NCBI_Build"
[5] "Chromosome" "Start_Position" "End_Position" "Strand"
[9] "Consequence" "Variant_Classification" "Variant_Type" "Reference_Allele"
[13] "Tumor_Seq_Allele1" "Tumor_Seq_Allele2" "dbSNP_RS" "dbSNP_Val_Status"
[17] "Tumor_Sample_Barcode" "Matched_Norm_Sample_Barcode" "Match_Norm_Seq_Allele1" "Match_Norm_Seq_Allele2"
[21] "Tumor_Validation_Allele1" "Tumor_Validation_Allele2" "Match_Norm_Validation_Allele1" "Match_Norm_Validation_Allele2"
[25] "Verification_Status" "Validation_Status" "Mutation_Status" "Sequencing_Phase"
[29] "Sequence_Source" "Validation_Method" "Score" "BAM_File"
[33] "Sequencer" "t_ref_count" "t_alt_count" "n_ref_count"
[37] "n_alt_count" "HGVSc" "HGVSp" "HGVSp_Short"
[41] "Transcript_ID" "RefSeq" "Protein_position" "Codons"
[45] "Exon_Number" "gnomAD_AF" "gnomAD_AFR_AF" "gnomAD_AMR_AF"
[49] "gnomAD_ASJ_AF" "gnomAD_EAS_AF" "gnomAD_FIN_AF" "gnomAD_NFE_AF"
[53] "gnomAD_OTH_AF" "gnomAD_SAS_AF" "FILTER" "Polyphen_Prediction"
[57] "Polyphen_Score" "SIFT_Prediction" "SIFT_Score" "SWISSPROT"
[61] "n_depth" "t_depth" "Annotation_Status" "mutationInCis_Flag"