[Bioc-devel] GenomeInfoDb is breaking bumphunter

Samuela Pollack @po||@ck @end|ng |rom j|mmy@h@rv@rd@edu
Wed Feb 13 16:00:18 CET 2019

Dear Bioconductor,

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?


- Sam

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
> [This is an automatically generated email. Please don't reply.]
> 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:
>        https://master.bioconductor.org/checkResults/3.8/bioc-LATEST/bumphunter/malbec1-checksrc.html
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
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