I have a granges object that I'm trying to export as a BigWig. The object looks like this:

> prediction
GRanges object with 4127167 ranges and 1 metadata column:
            seqnames              ranges strand |             score
               <Rle>           <IRanges>  <Rle> |         <numeric>
        [1]     chr1           5201-5400      * | 0.704062535636186
        [2]     chr1           5401-5600      * |   0.7038285233713
        [3]     chr1           5601-5800      * | 0.703379269216662
        [4]     chr1           5801-6000      * | 0.703339211770708
        [5]     chr1           6001-6200      * | 0.703186993302055
        ...      ...                 ...    ... .               ...
  [4127163]     chrX 155190601-155190800      * |   0.3657433841594
  [4127164]     chrX 155190801-155191000      * | 0.365798827160496
  [4127165]     chrX 155191001-155191200      * | 0.366063557897697
  [4127166]     chrX 155191201-155191400      * | 0.366739565616863
  [4127167]     chrX 155191401-155191600      * | 0.367196219763251
  -------
  seqinfo: 23 sequences from hg19 genome

> seqinfo(prediction)
Seqinfo object with 23 sequences from hg19 genome:
  seqnames seqlengths isCircular genome
  chr1      249250621       <NA>   hg19
  chr2      243199373       <NA>   hg19
  chr3      198022430       <NA>   hg19
  chr4      191154276       <NA>   hg19
  chr5      180915260       <NA>   hg19
  ...             ...        ...    ...
  chr19      59128983       <NA>   hg19
  chr20      63025520       <NA>   hg19
  chr21      48129895       <NA>   hg19
  chr22      51304566       <NA>   hg19
  chrX      155270560       <NA>   hg19

I have been using the export.bw feature from the rtracklayer R package in other cases successfully but for this case I run into an error that states:

>  rtracklayer::export.bw(prediction, con = "file.bw")
Error in FUN(extractROWS(unlisted_X, IRanges(X_elt_start[i], X_elt_end[i])),  : 
  Features cannot overlap. Note that WIG does not distinguish between strands - try exporting two tracks, one for each strand.

From what I see there aren't overlapping regions? All widths of the ranges are set at 200bps. Is there a way to check and remove/fix overlapping ranges?

EDIT: I've also tried to export by each chromosome split out and was returned a similar error:

prediction_by_chr <- split(prediction, f = seqnames(prediction))
lapply(seq_along(prediction_by_chr), function(x){
  chr <- names(prediction_by_chr)[x]; message(chr)
  rtracklayer::export.bw(prediction_by_chr[[chr]], con = "file.bw")  
})

Error in FUN(extractROWS(unlisted_X, IRanges(X_elt_start[i], X_elt_end[i])),  : 
  BigWig ranges cannot overlap

EDIT2: This solution seems to fix the issue by removing those overlaps:

hits <- findOverlaps(prediction, prediction)
overlaps <- hits[hits@from != hits@to]
o <- data.frame(seqnames = unlist(extractList(seqnames(prediction), overlaps)), 
                start = unlist(extractList(start(prediction), overlaps)), 
                end = unlist(extractList(end(prediction), overlaps)))
o_gr <- GenomicRanges::makeGRangesFromDataFrame(o)
prediction_fixed <- prediction[!(prediction %over% o_gr)]

You can drop the overlapping ranges with something like:

hits <- findOverlaps(prediction, drop.self=TRUE)
prediction_fixed <- prediction[-queryHits(hits)]