I've been trying to run CopywriteR, which requires S4Vectors to run.
after it creates the bam and bed files, it throws the error below:
lement index: 1, 2, 3, 4, 5, 6, ... first error: could not find function "subjectHits"
I thought it was because I didn't have installed S4Vectors, but it made no difference once I installed it.
then I read that from version 0.10 (https://github.com/Bioconductor/S4Vectors/blob/master/NEWS) the
subjectHits function was changed to the
I installed then the 0.8.11 version but now I get
1: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘S4Vectors’ 2: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘S4Vectors’ 3: no function found corresponding to methods exports from ‘IRanges’ for: ‘elementNROWS’, ‘from’, ‘nLnode’, ‘nRnode’, ‘pcompare’, ‘pcompareRecursively’, ‘relistToClass’, ‘to’ Execution halted
which tells me (maybe?) that the new S4Vectors knew to redirect the
subjectHits onto the
to function (and that's what it was expecting?).
so...I'm kinda of stuck, I cannot find out what happened and how I can get around this..and it's frustrating because CopywriteR runs for like 7hrs on all files but cannot finish the analysis.