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sellis18
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@sellis18-12319
Last seen 7.7 years ago
Receiving the following error message anytime I try to run findOverlaps() ...was working before update.
Error in validObject(.Object) : invalid class “IRanges” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")
Sorry for my super abbreviated post.
I agree that package updating is likely the culprit, but I also can't figure out if the build error on the most recent version of R for GenomicRanges could be causing the problem instead?
I'm currently using R-3.3.1.
Looking for overlaps between two GRanges objects:
> gtex_regions GRanges object with 7149 ranges and 6 metadata columns: > sra_regions GRanges object with 7149 ranges and 0 metadata columns: > ov <- GenomicRanges::findOverlaps(gtex_regions,sra_regions) Error in validObject(.Object) : invalid class “PartitioningByEnd” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")
Thanks for the first suggestion. Definitely a good check and something I hadn't done.:
Lastly, I was having the issue in R-devel also ....but I'll try working there. For now, here is sessionInfo() in case something is glaringly obvious...:
The even numbered 'y' of x.y.z versions in your Bioconductor packages indicate that you are working in the 'release' branch, so the build failure in the devel branch (the one that you pointed to, Bioconductor version 3.5) is not relevant. Also, the error that you reported, about DataTable_OR_NULL would only come from a devel package. So I guess the sessionInfo() you report above is not from the session where the bug was observed, or you've sometimes installed devel packages and then replaced them with release packages, or...?
Using biocLite() and the procedures recommended on each package landing page is a good way to avoid problems. Following the guidelines on http://bioconductor.org/developers/how-to/useDevel/ (these guidelines depend on release cycle) is the right way to use the devel version of Bioconductor.