Hi I tried to run the example in the getting started session and get warnings message and error using the data provided by HoneyBADGER. I followed this session exactly as shown in the website https://jef.works/HoneyBADGER/Getting_Started.html. This the warning messages I got were:
hb$setGeneFactors(txdb)

Warning messages:
1: In ifelse(strand(psF) == "+", 1, -1) * (start(peaks[!na.idx]) - :
longer object length is not a multiple of shorter object length
2: In ifelse(strand(peF) == "+", 1, -1) * (end(peaks[!na.idx]) - start(peF)) :
longer object length is not a multiple of shorter object length

I think that might be the reason that I got the following error when I ran

hb$retestIdentifiedCnvs(retestBoundGenes=TRUE, retestBoundSnps=TRUE, verbose=FALSE)
The error is
Error in as.vector(x) : no method for coercing this S4 class to a vector

Could you please help to have a look why I got these messages when I ran the example? Thank you very much!