[Bioc-devel] GenomeInfoDb is breaking bumphunter
@po||@ck @end|ng |rom j|mmy@h@rv@rd@edu
Wed Feb 13 16:00:18 CET 2019
The GenomeInfoDb package is generating an error in 3.8 and causing our
package bumphunter to crash too.
Our test calls GenomeInfoDb::fetchExtendedChromInfoDb and crashes with
an error that says some UCSC seqlevels in hg38 couldn't be mapped to
NCBI seqlevels. The release version of GenomeInfoDb is crashing in the
same function with the same error message.
The github repo for GenomeInfoDb indicates some work was done on this
routine two days ago. It looks like maybe we need a way to set the
drop_unmapped flag? Is that possible? What would you recommend?
On 2/12/19 12:55 PM, Rafael Irizarry wrote:
> see below
> ---------- Forwarded message ---------
> From: <BBS-noreply using bioconductor.org>
> Date: Tue, Feb 12, 2019 at 12:48 PM
> Subject: bumphunter problems reported in the Multiple platform
> build/check report for BioC 3.8
> To: <rafa using jimmy.harvard.edu>
> External Email - Use Caution
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> Hi bumphunter maintainer,
> According to the Multiple platform build/check report for BioC 3.8,
> the bumphunter package has the following problem(s):
> o ERROR for 'R CMD check' on malbec1. See the details here:
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
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