[Bioc-devel] GenomeInfoDb is breaking bumphunter
Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Wed Feb 13 16:06:57 CET 2019
Herve implemented a fix in release and devel as indicated by the support site question
It has yet to propagate to the system but should be up later today.
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Samuela Pollack <spollack using jimmy.harvard.edu>
Sent: Wednesday, February 13, 2019 10:00:18 AM
To: Rafael Irizarry; Leonardo Collado Torres; Bioc-devel
Subject: [Bioc-devel] GenomeInfoDb is breaking bumphunter
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
> [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:
> Please take the time to address this by committing and pushing
> changes to your package at git.bioconductor.org
> * This was the status of your package at the time this email was sent to you.
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