hi all
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 to
function
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.
thanks!
Indeed, our CopywriteR package does depend on subjectHits, but since a small test sample is run during building for the vignette, all the dependencies should be fine. Is it possible to install CopywriteR again using the biocLite tool:
If this does not help please let us know.