Question

Error with findOverlapsOfPeaks

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alex.tamburino • 0

@alextamburino-10105

Last seen 8.0 years ago

Hi, I am getting the following error. Any ideas? Thanks

>findOverlapsOfPeaks(gr1,gr2)

Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : 
  object 'orderInteger' not found

> gr1

GRanges object with 6122 ranges and 1 metadata column:
        seqnames               ranges strand |       score
           <Rle>            <IRanges>  <Rle> |   <numeric>
     X0        1     [ 10076,  10388]      + | 7.030091837
     X1        1     [ 34857,  34953]      + | 16.00229019
     X2        1     [137436, 137504]      + | 33.09947392
     X3        1     [205373, 205469]      + | 16.54973696
     X4        1     [258727, 258804]      + | 27.74514726
    ...      ...                  ...    ... .         ...
  X6117        Y [56770157, 56770285]      + | 9.035775927
  X6118        Y [56771048, 56771241]      + | 12.33025828
  X6119        Y [56827831, 56827998]      + | 11.55585383
  X6120        Y [56832012, 56832271]      + | 8.348097405
  X6121        Y [56832585, 56833014]      + |  6.87515344

ChIPpeakAnno • 1.0k views

ADD COMMENT • link 8.0 years ago alex.tamburino • 0

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I'd guess that you had a package version mis-match. Does BiocInstaller::biocValid() identify packages that are too old or new for the version of Bioconductor you have in use? If so, does it help to follow the suggestions in the output to remedy the situation?

ADD REPLY • link 8.0 years ago Martin Morgan 25k