[Bioc-devel] GenomicRanges distanceToNearest() causing issues

[Martin Morgan]

Hi Raymond -- Daniel provides a fix for this and ported it to release, 
but it has failed to propagate for complicated git-related reasons. I 
believe that installing from source

   git clone https://git.bioconductor.org/packages/GenomicRanges
   cd GenomicRanges
   git checkout RELEASE_3_6
   R CMD INSTALL .

or from github

   biocLite("Bioconductor/GenomicRanges", ref="RELEASE_3_6")

will work.

The release binary should propagate Sunday or Monday (there is a 
remaining problem, and it might not be fixed in time for the start of 
tonight's builds).

Martin


On 02/24/2018 01:35 PM, Raymond Cavalcante wrote:
> Hello,
> 
> 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?
> 
> Thanks,
> Raymond Cavalcante
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