[Bioc-devel] GenomicRanges distanceToNearest() causing issues

Raymond Cavalcante rcavalca at umich.edu
Sat Feb 24 19:35:36 CET 2018


I’m the maintainer of the chipenrich package which has had a TIMEOUT error for quite a while now. I’ve traced the problem to GenomicRanges::distanceToNearest() which appears to have broken between versions 1.30.0 and 1.30.1. 

I’m experimenting on the R Bioconductor 3.6 Release Docker image with up-to-date packages. I manually installed Genomic Ranges 1.30.0 and chipenrich 2.2.0 builds without issue in a reasonable amount of time. I then manually installed GenomicRanges 1.30.1, and the same chipenrich 2.2.0 takes a *very* long time to build (eventually finishing, but not in enough time for the Bioc build system).

I thought one possible problem might stem from having slightly different seqinfo() attributes in the GRanges used in distanceToNearest(). However, when I coerce their seqinfo() to be identical the distanceToNearest() takes a *very* long time.

Do any Bioconductor team members have any news as to the status of this problem?

Raymond Cavalcante

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