Hi everyone, I was hoping someone might be able to help me with an issue I am having.

I am changing the imports in my NAMESPACE file from imports to importsFrom, and everything runs correctly when I specify import(GenomicRanges). However, when I use importFrom(GenomicRanges, GRanges) and importFrom(GenomicRanges, findOverlaps) I get the below error:

"error in evaluating the argument 'query' in selecting a method for function 'findOverlaps': each range must have an end that is greater or equal to its start minus one"

This seemed strange to me because it only appears when I don't import the full package. I have also included all of my other namespace imports below. Does anyone know why this could be? Thank you in advance!

importFrom(AnnotationDbi,select)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,genes)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,findOverlaps)
importFrom(IRanges,IRanges)
importFrom(IRanges,overlapsAny)
importFrom(Repitools,annoGR2DF)
importFrom(S4Vectors,Rle)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(TxDb.Hsapiens.UCSC.hg19.knownGene,TxDb.Hsapiens.UCSC.hg19.knownGene)
importFrom(TxDb.Hsapiens.UCSC.hg38.knownGene,TxDb.Hsapiens.UCSC.hg38.knownGene)
importFrom(org.Hs.eg.db,org.Hs.eg.db)

sessionInfo( )

You should probably ask this at bioc-devel@r-project.org, as it's a developer question. That said, you get this error

"error in evaluating the argument 'query' in selecting a method for function 'findOverlaps':

Which may indicate that the findOverlaps function you are looking for isn't from GenomicRanges, but instead from a different package. Which depends on the query (and subject) arguments. For example

> library(GenomicRanges)
> showMethods(findOverlaps)
Function: findOverlaps (package IRanges)
query="ANY", subject="Pairs"
query="GenomicRanges", subject="GenomicRanges"
query="GenomicRanges", subject="GRangesList"
query="GRangesList", subject="GenomicRanges"
query="GRangesList", subject="GRangesList"
query="integer", subject="IntegerRanges"
query="IntegerRanges", subject="IntegerRanges"
query="IntegerRangesList", subject="IntegerRangesList"
query="Pairs", subject="ANY"
query="Pairs", subject="missing"
query="Pairs", subject="Pairs"
query="Vector", subject="missing"

> selectMethod(findOverlaps, c(query="IntegerRanges", subject="IntegerRanges"))
Method Definition:

function (query, subject, maxgap = -1L, minoverlap = 0L, type = c("any", 
    "start", "end", "within", "equal"), select = c("all", "first", 
    "last", "arbitrary"), ...) 
{
    .local <- function (query, subject, maxgap = -1L, minoverlap = 0L, 
        type = c("any", "start", "end", "within", "equal"), select = c("all", 
            "first", "last", "arbitrary")) 
    {
        if (is.integer(query)) 
            query <- IRanges(query, width = 1L)
        type <- match.arg(type)
        select <- match.arg(select)
        findOverlaps_NCList(query, subject, maxgap = maxgap, 
            minoverlap = minoverlap, type = type, select = select)
    }
    .local(query, subject, maxgap, minoverlap, type, select, 
        ...)
}
<bytecode: 0x000001ea2d25b260>
<environment: namespace:IRanges>

Signatures:
        query           subject        
target  "IntegerRanges" "IntegerRanges"
defined "IntegerRanges" "IntegerRanges"

If your query is a IntegerRanges, then you probably don't have the right findOverlaps imported from GenomicRanges.