[Bioc-devel] Error with InteractionSet package

Ioannis Vardaxis ioannis.vardaxis at math.ntnu.no
Tue Nov 8 18:34:46 CET 2016


I am trying to combine two GRanges from two anchors of same length in to a Gitnteractions object and I get the following error:

> PairedData=InteractionSet::GInteractions(anchor1=Anchor1,anchor2=Anchor2)
Error in .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions,  :
  first and second anchor vectors have different lengths
> length(Anchor1)
[1] 33705839
> length(Anchor2)
[1] 33705839
> traceback()
5: stop(msg)
4: .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions,
       metadata = metadata, mode = mode)
3: .local(anchor1, anchor2, regions, ...)
2: InteractionSet::GInteractions(anchor1 = Anchor1, anchor2 = Anchor2)
1: InteractionSet::GInteractions(anchor1 = Anchor1, anchor2 = Anchor2)

While they clearly have the same length.

If I then run it again it works fine.

If I then run again one more time I get:
Error in .new_GInteractions(anchor1 = anchor1, anchor2 = anchor2, regions = regions,  :
  all anchor indices must be finite integers
In addition: Warning message:
In new.pos[o] <- new.pos :
  number of items to replace is not a multiple of replacement length

I run it again and I get the correct results.

It seems like it is quite random if I get en error or not.

Ioannis Vardaxis
Stipendiat IMF

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