ChIPSeeker failing

I cannot run ChIPSeeker the job keep failing, I think its due to the format of annotation source (I used gtf format?)
this is the message from the job after it failed:
Import genomic features from the file as a GRanges object … OK Prepare the ‘metadata’ data frame … OK Make the TxDb object … OK Warning messages: 1: In .local(con, format, text, …) : gff-version directive indicates version is 3, not 2 2: In .extract_transcripts_from_GRanges(tx_IDX, gr, type, ID, Name) : The following transcripts have multiple parts that were merged: Error in [<*tmp*, tssIndex, “Promoter”, value = TRUE) : replacement has 1 row, data has 0 Calls: annotatePeak → getGenomicAnnotation → [<- → [<

Can you help me what the problem???